Data items in the ATOM_SITE category record details about the atom sites in a macromolecular crystal structure, such as the positional coordinates, atomic displacement parameters, magnetic moments and directions, and so on. The data items for describing anisotropic temperature or atomic displacement factors are only used if the corresponding items are not given in the ATOM_SITE_ANISOTROP category. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:atom_siteCategory> <PDBx:atom_site id="1"> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:type_symbol>N</PDBx:type_symbol> <PDBx:label_atom_id>N</PDBx:label_atom_id> <PDBx:label_comp_id>VAL</PDBx:label_comp_id> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_seq_id>11</PDBx:label_seq_id> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:Cartn_x>25.369</PDBx:Cartn_x> <PDBx:Cartn_y>30.691</PDBx:Cartn_y> <PDBx:Cartn_z>11.795</PDBx:Cartn_z> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:B_iso_or_equiv>17.93</PDBx:B_iso_or_equiv> <PDBx:auth_seq_id>11</PDBx:auth_seq_id> </PDBx:atom_site> <PDBx:atom_site id="2"> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:label_atom_id>CA</PDBx:label_atom_id> <PDBx:label_comp_id>VAL</PDBx:label_comp_id> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_seq_id>11</PDBx:label_seq_id> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:Cartn_x>25.970</PDBx:Cartn_x> <PDBx:Cartn_y>31.965</PDBx:Cartn_y> <PDBx:Cartn_z>12.332</PDBx:Cartn_z> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:B_iso_or_equiv>17.75</PDBx:B_iso_or_equiv> <PDBx:auth_seq_id>11</PDBx:auth_seq_id> </PDBx:atom_site> <PDBx:atom_site id="3"> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:label_atom_id>C</PDBx:label_atom_id> <PDBx:label_comp_id>VAL</PDBx:label_comp_id> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_seq_id>11</PDBx:label_seq_id> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:Cartn_x>25.569</PDBx:Cartn_x> <PDBx:Cartn_y>32.010</PDBx:Cartn_y> <PDBx:Cartn_z>13.808</PDBx:Cartn_z> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:B_iso_or_equiv>17.83</PDBx:B_iso_or_equiv> <PDBx:auth_seq_id>11</PDBx:auth_seq_id> </PDBx:atom_site> <PDBx:atom_site id="4"> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:type_symbol>O</PDBx:type_symbol> <PDBx:label_atom_id>O</PDBx:label_atom_id> <PDBx:label_comp_id>VAL</PDBx:label_comp_id> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_seq_id>11</PDBx:label_seq_id> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:Cartn_x>24.735</PDBx:Cartn_x> <PDBx:Cartn_y>31.190</PDBx:Cartn_y> <PDBx:Cartn_z>14.167</PDBx:Cartn_z> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:B_iso_or_equiv>17.53</PDBx:B_iso_or_equiv> <PDBx:auth_seq_id>11</PDBx:auth_seq_id> </PDBx:atom_site> <PDBx:atom_site id="5"> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:label_atom_id>CB</PDBx:label_atom_id> <PDBx:label_comp_id>VAL</PDBx:label_comp_id> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_seq_id>11</PDBx:label_seq_id> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:Cartn_x>25.379</PDBx:Cartn_x> <PDBx:Cartn_y>33.146</PDBx:Cartn_y> <PDBx:Cartn_z>11.540</PDBx:Cartn_z> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:B_iso_or_equiv>17.66</PDBx:B_iso_or_equiv> <PDBx:auth_seq_id>11</PDBx:auth_seq_id> </PDBx:atom_site> <PDBx:atom_site id="6"> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:label_atom_id>CG1</PDBx:label_atom_id> <PDBx:label_comp_id>VAL</PDBx:label_comp_id> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_seq_id>11</PDBx:label_seq_id> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:Cartn_x>25.584</PDBx:Cartn_x> <PDBx:Cartn_y>33.034</PDBx:Cartn_y> <PDBx:Cartn_z>10.030</PDBx:Cartn_z> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:B_iso_or_equiv>18.86</PDBx:B_iso_or_equiv> <PDBx:auth_seq_id>11</PDBx:auth_seq_id> </PDBx:atom_site> <PDBx:atom_site id="7"> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:label_atom_id>CG2</PDBx:label_atom_id> <PDBx:label_comp_id>VAL</PDBx:label_comp_id> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_seq_id>11</PDBx:label_seq_id> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:Cartn_x>23.933</PDBx:Cartn_x> <PDBx:Cartn_y>33.309</PDBx:Cartn_y> <PDBx:Cartn_z>11.872</PDBx:Cartn_z> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:B_iso_or_equiv>17.12</PDBx:B_iso_or_equiv> <PDBx:auth_seq_id>11</PDBx:auth_seq_id> </PDBx:atom_site> <PDBx:atom_site id="8"> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:type_symbol>N</PDBx:type_symbol> <PDBx:label_atom_id>N</PDBx:label_atom_id> <PDBx:label_comp_id>THR</PDBx:label_comp_id> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_seq_id>12</PDBx:label_seq_id> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:Cartn_x>26.095</PDBx:Cartn_x> <PDBx:Cartn_y>32.930</PDBx:Cartn_y> <PDBx:Cartn_z>14.590</PDBx:Cartn_z> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:B_iso_or_equiv>18.97</PDBx:B_iso_or_equiv> <PDBx:footnote_id>4</PDBx:footnote_id> <PDBx:auth_seq_id>12</PDBx:auth_seq_id> </PDBx:atom_site> <PDBx:atom_site id="9"> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:label_atom_id>CA</PDBx:label_atom_id> <PDBx:label_comp_id>THR</PDBx:label_comp_id> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_seq_id>12</PDBx:label_seq_id> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:Cartn_x>25.734</PDBx:Cartn_x> <PDBx:Cartn_y>32.995</PDBx:Cartn_y> <PDBx:Cartn_z>16.032</PDBx:Cartn_z> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:B_iso_or_equiv>19.80</PDBx:B_iso_or_equiv> <PDBx:footnote_id>4</PDBx:footnote_id> <PDBx:auth_seq_id>12</PDBx:auth_seq_id> </PDBx:atom_site> <PDBx:atom_site id="10"> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:label_atom_id>C</PDBx:label_atom_id> <PDBx:label_comp_id>THR</PDBx:label_comp_id> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_seq_id>12</PDBx:label_seq_id> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:Cartn_x>24.695</PDBx:Cartn_x> <PDBx:Cartn_y>34.106</PDBx:Cartn_y> <PDBx:Cartn_z>16.113</PDBx:Cartn_z> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:B_iso_or_equiv>20.92</PDBx:B_iso_or_equiv> <PDBx:footnote_id>4</PDBx:footnote_id> <PDBx:auth_seq_id>12</PDBx:auth_seq_id> </PDBx:atom_site> <PDBx:atom_site id="11"> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:type_symbol>O</PDBx:type_symbol> <PDBx:label_atom_id>O</PDBx:label_atom_id> <PDBx:label_comp_id>THR</PDBx:label_comp_id> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_seq_id>12</PDBx:label_seq_id> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:Cartn_x>24.869</PDBx:Cartn_x> <PDBx:Cartn_y>35.118</PDBx:Cartn_y> <PDBx:Cartn_z>15.421</PDBx:Cartn_z> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:B_iso_or_equiv>21.84</PDBx:B_iso_or_equiv> <PDBx:footnote_id>4</PDBx:footnote_id> <PDBx:auth_seq_id>12</PDBx:auth_seq_id> </PDBx:atom_site> <PDBx:atom_site id="12"> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:label_atom_id>CB</PDBx:label_atom_id> <PDBx:label_comp_id>THR</PDBx:label_comp_id> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_seq_id>12</PDBx:label_seq_id> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:Cartn_x>26.911</PDBx:Cartn_x> <PDBx:Cartn_y>33.346</PDBx:Cartn_y> <PDBx:Cartn_z>17.018</PDBx:Cartn_z> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:B_iso_or_equiv>20.51</PDBx:B_iso_or_equiv> <PDBx:footnote_id>4</PDBx:footnote_id> <PDBx:auth_seq_id>12</PDBx:auth_seq_id> </PDBx:atom_site> <PDBx:atom_site id="13"> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:type_symbol>O</PDBx:type_symbol> <PDBx:label_atom_id>OG1</PDBx:label_atom_id> <PDBx:label_comp_id>THR</PDBx:label_comp_id> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_seq_id>12</PDBx:label_seq_id> <PDBx:label_alt_id>3</PDBx:label_alt_id> <PDBx:Cartn_x>27.946</PDBx:Cartn_x> <PDBx:Cartn_y>33.921</PDBx:Cartn_y> <PDBx:Cartn_z>16.183</PDBx:Cartn_z> <PDBx:occupancy>0.50</PDBx:occupancy> <PDBx:B_iso_or_equiv>20.29</PDBx:B_iso_or_equiv> <PDBx:footnote_id>4</PDBx:footnote_id> <PDBx:auth_seq_id>12</PDBx:auth_seq_id> </PDBx:atom_site> <PDBx:atom_site id="14"> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:type_symbol>O</PDBx:type_symbol> <PDBx:label_atom_id>OG1</PDBx:label_atom_id> <PDBx:label_comp_id>THR</PDBx:label_comp_id> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_seq_id>12</PDBx:label_seq_id> <PDBx:label_alt_id>4</PDBx:label_alt_id> <PDBx:Cartn_x>27.769</PDBx:Cartn_x> <PDBx:Cartn_y>32.142</PDBx:Cartn_y> <PDBx:Cartn_z>17.103</PDBx:Cartn_z> <PDBx:occupancy>0.50</PDBx:occupancy> <PDBx:B_iso_or_equiv>20.59</PDBx:B_iso_or_equiv> <PDBx:footnote_id>4</PDBx:footnote_id> <PDBx:auth_seq_id>12</PDBx:auth_seq_id> </PDBx:atom_site> <PDBx:atom_site id="15"> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:label_atom_id>CG2</PDBx:label_atom_id> <PDBx:label_comp_id>THR</PDBx:label_comp_id> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_seq_id>12</PDBx:label_seq_id> <PDBx:label_alt_id>3</PDBx:label_alt_id> <PDBx:Cartn_x>27.418</PDBx:Cartn_x> <PDBx:Cartn_y>32.181</PDBx:Cartn_y> <PDBx:Cartn_z>17.878</PDBx:Cartn_z> <PDBx:occupancy>0.50</PDBx:occupancy> <PDBx:B_iso_or_equiv>20.47</PDBx:B_iso_or_equiv> <PDBx:footnote_id>4</PDBx:footnote_id> <PDBx:auth_seq_id>12</PDBx:auth_seq_id> </PDBx:atom_site> <PDBx:atom_site id="16"> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:label_atom_id>CG2</PDBx:label_atom_id> <PDBx:label_comp_id>THR</PDBx:label_comp_id> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_seq_id>12</PDBx:label_seq_id> <PDBx:label_alt_id>4</PDBx:label_alt_id> <PDBx:Cartn_x>26.489</PDBx:Cartn_x> <PDBx:Cartn_y>33.778</PDBx:Cartn_y> <PDBx:Cartn_z>18.426</PDBx:Cartn_z> <PDBx:occupancy>0.50</PDBx:occupancy> <PDBx:B_iso_or_equiv>20.00</PDBx:B_iso_or_equiv> <PDBx:footnote_id>4</PDBx:footnote_id> <PDBx:auth_seq_id>12</PDBx:auth_seq_id> </PDBx:atom_site> <PDBx:atom_site id="17"> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:type_symbol>N</PDBx:type_symbol> <PDBx:label_atom_id>N</PDBx:label_atom_id> <PDBx:label_comp_id>ILE</PDBx:label_comp_id> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_seq_id>13</PDBx:label_seq_id> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:Cartn_x>23.664</PDBx:Cartn_x> <PDBx:Cartn_y>33.855</PDBx:Cartn_y> <PDBx:Cartn_z>16.884</PDBx:Cartn_z> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:B_iso_or_equiv>22.08</PDBx:B_iso_or_equiv> <PDBx:auth_seq_id>13</PDBx:auth_seq_id> </PDBx:atom_site> <PDBx:atom_site id="18"> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:label_atom_id>CA</PDBx:label_atom_id> <PDBx:label_comp_id>ILE</PDBx:label_comp_id> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_seq_id>13</PDBx:label_seq_id> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:Cartn_x>22.623</PDBx:Cartn_x> <PDBx:Cartn_y>34.850</PDBx:Cartn_y> <PDBx:Cartn_z>17.093</PDBx:Cartn_z> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:B_iso_or_equiv>23.44</PDBx:B_iso_or_equiv> <PDBx:auth_seq_id>13</PDBx:auth_seq_id> </PDBx:atom_site> <PDBx:atom_site id="19"> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:label_atom_id>C</PDBx:label_atom_id> <PDBx:label_comp_id>ILE</PDBx:label_comp_id> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_seq_id>13</PDBx:label_seq_id> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:Cartn_x>22.657</PDBx:Cartn_x> <PDBx:Cartn_y>35.113</PDBx:Cartn_y> <PDBx:Cartn_z>18.610</PDBx:Cartn_z> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:B_iso_or_equiv>25.77</PDBx:B_iso_or_equiv> <PDBx:auth_seq_id>13</PDBx:auth_seq_id> </PDBx:atom_site> <PDBx:atom_site id="20"> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:type_symbol>O</PDBx:type_symbol> <PDBx:label_atom_id>O</PDBx:label_atom_id> <PDBx:label_comp_id>ILE</PDBx:label_comp_id> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_seq_id>13</PDBx:label_seq_id> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:Cartn_x>23.123</PDBx:Cartn_x> <PDBx:Cartn_y>34.250</PDBx:Cartn_y> <PDBx:Cartn_z>19.406</PDBx:Cartn_z> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:B_iso_or_equiv>26.28</PDBx:B_iso_or_equiv> <PDBx:auth_seq_id>13</PDBx:auth_seq_id> </PDBx:atom_site> <PDBx:atom_site id="21"> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:label_atom_id>CB</PDBx:label_atom_id> <PDBx:label_comp_id>ILE</PDBx:label_comp_id> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_seq_id>13</PDBx:label_seq_id> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:Cartn_x>21.236</PDBx:Cartn_x> <PDBx:Cartn_y>34.463</PDBx:Cartn_y> <PDBx:Cartn_z>16.492</PDBx:Cartn_z> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:B_iso_or_equiv>22.67</PDBx:B_iso_or_equiv> <PDBx:auth_seq_id>13</PDBx:auth_seq_id> </PDBx:atom_site> <PDBx:atom_site id="22"> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:label_atom_id>CG1</PDBx:label_atom_id> <PDBx:label_comp_id>ILE</PDBx:label_comp_id> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_seq_id>13</PDBx:label_seq_id> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:Cartn_x>20.478</PDBx:Cartn_x> <PDBx:Cartn_y>33.469</PDBx:Cartn_y> <PDBx:Cartn_z>17.371</PDBx:Cartn_z> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:B_iso_or_equiv>22.14</PDBx:B_iso_or_equiv> <PDBx:auth_seq_id>13</PDBx:auth_seq_id> </PDBx:atom_site> <PDBx:atom_site id="23"> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:label_atom_id>CG2</PDBx:label_atom_id> <PDBx:label_comp_id>ILE</PDBx:label_comp_id> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_seq_id>13</PDBx:label_seq_id> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:Cartn_x>21.357</PDBx:Cartn_x> <PDBx:Cartn_y>33.986</PDBx:Cartn_y> <PDBx:Cartn_z>15.016</PDBx:Cartn_z> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:B_iso_or_equiv>21.75</PDBx:B_iso_or_equiv> <PDBx:auth_seq_id>13</PDBx:auth_seq_id> </PDBx:atom_site> <PDBx:atom_site id="101"> <PDBx:group_PDB>HETATM</PDBx:group_PDB> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:label_atom_id>C1</PDBx:label_atom_id> <PDBx:label_comp_id>APS</PDBx:label_comp_id> <PDBx:label_asym_id>C</PDBx:label_asym_id> <PDBx:label_seq_id xsi:nil="true" /> <PDBx:label_alt_id>1</PDBx:label_alt_id> <PDBx:Cartn_x>4.171</PDBx:Cartn_x> <PDBx:Cartn_y>29.012</PDBx:Cartn_y> <PDBx:Cartn_z>7.116</PDBx:Cartn_z> <PDBx:occupancy>0.58</PDBx:occupancy> <PDBx:B_iso_or_equiv>17.27</PDBx:B_iso_or_equiv> <PDBx:footnote_id>1</PDBx:footnote_id> <PDBx:auth_seq_id>300</PDBx:auth_seq_id> </PDBx:atom_site> <PDBx:atom_site id="102"> <PDBx:group_PDB>HETATM</PDBx:group_PDB> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:label_atom_id>C2</PDBx:label_atom_id> <PDBx:label_comp_id>APS</PDBx:label_comp_id> <PDBx:label_asym_id>C</PDBx:label_asym_id> <PDBx:label_seq_id xsi:nil="true" /> <PDBx:label_alt_id>1</PDBx:label_alt_id> <PDBx:Cartn_x>4.949</PDBx:Cartn_x> <PDBx:Cartn_y>27.758</PDBx:Cartn_y> <PDBx:Cartn_z>6.793</PDBx:Cartn_z> <PDBx:occupancy>0.58</PDBx:occupancy> <PDBx:B_iso_or_equiv>16.95</PDBx:B_iso_or_equiv> <PDBx:footnote_id>1</PDBx:footnote_id> <PDBx:auth_seq_id>300</PDBx:auth_seq_id> </PDBx:atom_site> <PDBx:atom_site id="103"> <PDBx:group_PDB>HETATM</PDBx:group_PDB> <PDBx:type_symbol>O</PDBx:type_symbol> <PDBx:label_atom_id>O3</PDBx:label_atom_id> <PDBx:label_comp_id>APS</PDBx:label_comp_id> <PDBx:label_asym_id>C</PDBx:label_asym_id> <PDBx:label_seq_id xsi:nil="true" /> <PDBx:label_alt_id>1</PDBx:label_alt_id> <PDBx:Cartn_x>4.800</PDBx:Cartn_x> <PDBx:Cartn_y>26.678</PDBx:Cartn_y> <PDBx:Cartn_z>7.393</PDBx:Cartn_z> <PDBx:occupancy>0.58</PDBx:occupancy> <PDBx:B_iso_or_equiv>16.85</PDBx:B_iso_or_equiv> <PDBx:footnote_id>1</PDBx:footnote_id> <PDBx:auth_seq_id>300</PDBx:auth_seq_id> </PDBx:atom_site> <PDBx:atom_site id="104"> <PDBx:group_PDB>HETATM</PDBx:group_PDB> <PDBx:type_symbol>N</PDBx:type_symbol> <PDBx:label_atom_id>N4</PDBx:label_atom_id> <PDBx:label_comp_id>APS</PDBx:label_comp_id> <PDBx:label_asym_id>C</PDBx:label_asym_id> <PDBx:label_seq_id xsi:nil="true" /> <PDBx:label_alt_id>1</PDBx:label_alt_id> <PDBx:Cartn_x>5.930</PDBx:Cartn_x> <PDBx:Cartn_y>27.841</PDBx:Cartn_y> <PDBx:Cartn_z>5.869</PDBx:Cartn_z> <PDBx:occupancy>0.58</PDBx:occupancy> <PDBx:B_iso_or_equiv>16.43</PDBx:B_iso_or_equiv> <PDBx:footnote_id>1</PDBx:footnote_id> <PDBx:auth_seq_id>300</PDBx:auth_seq_id> </PDBx:atom_site> </PDBx:atom_siteCategory> Equivalent isotropic atomic displacement parameter, B~equiv~, in angstroms squared, calculated as the geometric mean of the anisotropic atomic displacement parameters. B~equiv~ = (B~i~ B~j~ B~k~)^1/3^ B~n~ = the principal components of the orthogonalised B^ij^ The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. The estimated standard deviation of attribute B_equiv_geom_mean in category atom_site. Isotropic temperature factor parameter, or equivalent isotropic temperature factor, B~equiv~, calculated from anisotropic temperature factor parameters. B~equiv~ = (1/3) sum~i~[sum~j~(B~ij~ A~i~ A~j~ a*~i~ a*~j~)] A = the real space cell lengths a* = the reciprocal space cell lengths B~ij~ = 8 pi^2^ U~ij~ Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. The estimated standard deviation of attribute B_iso_or_equiv in category atom_site. The x atom site coordinate in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the description given in attribute Cartn_transform_axes in category atom_sites. The estimated standard deviation of attribute Cartn_x in category atom_site. The y atom site coordinate in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the description given in attribute Cartn_transform_axes in category atom_sites. The estimated standard deviation of attribute Cartn_y in category atom_site. The z atom site coordinate in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the description given in attribute Cartn_transform_axes in category atom_sites. The estimated standard deviation of attribute Cartn_z in category atom_site. Equivalent isotropic atomic displacement parameter, U~equiv~, in angstroms squared, calculated as the geometric mean of the anisotropic atomic displacement parameters. U~equiv~ = (U~i~ U~j~ U~k~)^1/3^ U~n~ = the principal components of the orthogonalised U~ij~ The estimated standard deviation of attribute U_equiv_geom_mean in category atom_site. Isotropic atomic displacement parameter, or equivalent isotropic atomic displacement parameter, U~equiv~, calculated from anisotropic atomic displacement parameters. U~equiv~ = (1/3) sum~i~[sum~j~(U~ij~ A~i~ A~j~ a*~i~ a*~j~)] A = the real space cell lengths a* = the reciprocal space cell lengths Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776. The estimated standard deviation of attribute U_iso_or_equiv in category atom_site. The Wyckoff symbol (letter) as listed in the space-group section of International Tables for Crystallography, Vol. A (1987). The [1][1] element of the anisotropic atomic displacement matrix B, which appears in the structure factor term as: T = exp{-1/4 sum~i~[sum~j~(B~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. The estimated standard deviation of attribute aniso_B[1][1] in category atom_site. The [1][2] element of the anisotropic atomic displacement matrix B, which appears in the structure factor term as: T = exp{-1/4 sum~i~[sum~j~(B~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. The estimated standard deviation of attribute aniso_B[1][2] in category atom_site. The [1][3] element of the anisotropic atomic displacement matrix B, which appears in the structure factor term as: T = exp{-1/4 sum~i~[sum~j~(B~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. The estimated standard deviation of attribute aniso_B[1][3] in category atom_site. The [2][2] element of the anisotropic atomic displacement matrix B, which appears in the structure factor term as: T = exp{-1/4 sum~i~[sum~j~(B~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. The estimated standard deviation of attribute aniso_B[2][2] in category atom_site. The [2][3] element of the anisotropic atomic displacement matrix B, which appears in the structure factor term as: T = exp{-1/4 sum~i~[sum~j~(B~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. The estimated standard deviation of attribute aniso_B[2][3] in category atom_site. The [3][3] element of the anisotropic atomic displacement matrix B, which appears in the structure factor term as: T = exp{-1/4 sum~i~[sum~j~(B~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. The estimated standard deviation of attribute aniso_B[3][3] in category atom_site. The [1][1] element of the standard anisotropic atomic displacement matrix U, which appears in the structure factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The estimated standard deviation of attribute aniso_U[1][1] in category atom_site. The [1][2] element of the standard anisotropic atomic displacement matrix U, which appears in the structure factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The estimated standard deviation of attribute aniso_U[1][2] in category atom_site. The [1][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The estimated standard deviation of attribute aniso_U[1][3] in category atom_site. The [2][2] element of the standard anisotropic atomic displacement matrix U, which appears in the structure factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The estimated standard deviation of attribute aniso_U[2][2] in category atom_site. The [2][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The estimated standard deviation of attribute aniso_U[2][3] in category atom_site. The [3][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The estimated standard deviation of attribute aniso_U[3][3] in category atom_site. Ratio of the maximum to minimum principal axes of displacement (thermal) ellipsoids. The number of hydrogen atoms attached to the atom at this site excluding any H atoms for which coordinates (measured or calculated) are given. water oxygen 2 hydroxyl oxygen 1 ammonium nitrogen 4 An alternative identifier for attribute label_asym_id in category atom_site that may be provided by an author in order to match the identification used in the publication that describes the structure. An alternative identifier for attribute label_atom_id in category atom_site that may be provided by an author in order to match the identification used in the publication that describes the structure. An alternative identifier for attribute label_comp_id in category atom_site that may be provided by an author in order to match the identification used in the publication that describes the structure. An alternative identifier for attribute label_seq_id in category atom_site that may be provided by an author in order to match the identification used in the publication that describes the structure. Note that this is not necessarily a number, that the values do not have to be positive, and that the value does not have to correspond to the value of attribute label_seq_id in category atom_site. The value of attribute label_seq_id in category atom_site is required to be a sequential list of positive integers. The author may assign values to attribute auth_seq_id in category atom_site in any desired way. For instance, the values may be used to relate this structure to a numbering scheme in a homologous structure, including sequence gaps or insertion codes. Alternatively, a scheme may be used for a truncated polymer that maintains the numbering scheme of the full length polymer. In all cases, the scheme used here must match the scheme used in the publication that describes the structure. The attribute id in category atom_site of the atom site to which the 'geometry- calculated' atom site is attached. A standard code to signal if the site data have been determined from the intensities or calculated from the geometry of surrounding sites, or have been assigned dummy coordinates. The abbreviation 'c' may be used in place of 'calc'. This data item is a pointer to attribute number in category chemical_conn_atom in the CHEMICAL_CONN_ATOM category. A description of the constraints applied to parameters at this site during refinement. See also attribute refinement_flags in category atom_site and attribute ls_number_constraints in category refine. pop=1.0-pop(Zn3) A description of special aspects of this site. See also attribute refinement_flags in category atom_site. Ag/Si disordered A code which identifies a cluster of atoms that show long-range positional disorder but are locally ordered. Within each such cluster of atoms, attribute disorder_group in category atom_site is used to identify the sites that are simultaneously occupied. This field is only needed if there is more than one cluster of disordered atoms showing independent local order. *** This data item would not in general be used in a macromolecular data block. *** A code that identifies a group of positionally disordered atom sites that are locally simultaneously occupied. Atoms that are positionally disordered over two or more sites (e.g. the H atoms of a methyl group that exists in two orientations) can be assigned to two or more groups. Sites belonging to the same group are simultaneously occupied, but those belonging to different groups are not. A minus prefix (e.g. "-1") is used to indicate sites disordered about a special position. *** This data item would not in general be used in a macromolecular data block. *** The value of attribute footnote_id in category atom_site must match an id specified by attribute id in category atom_sites_footnote in the ATOM_SITES_FOOTNOTE list. The x coordinate of the atom site position specified as a fraction of attribute length_a in category cell. The estimated standard deviation of attribute fract_x in category atom_site. The y coordinate of the atom site position specified as a fraction of attribute length_b in category cell. The estimated standard deviation of attribute fract_y in category atom_site. The z coordinate of the atom site position specified as a fraction of attribute length_c in category cell. The estimated standard deviation of attribute fract_z in category atom_site. The group of atoms to which the atom site belongs. This data item is provided for compatibility with the original Protein Data Bank format, and only for that purpose. A component of the macromolecular identifier for this atom site. For further details, see the definition of the ATOM_SITE_ALT category. This data item is a pointer to attribute id in category atom_sites_alt in the ATOM_SITES_ALT category. A component of the macromolecular identifier for this atom site. For further details, see the definition of the STRUCT_ASYM category. This data item is a pointer to attribute id in category struct_asym in the STRUCT_ASYM category. A component of the macromolecular identifier for this atom site. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. A component of the macromolecular identifier for this atom site. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. This data item is a pointer to attribute id in category entity in the ENTITY category. This data item is a pointer to attribute num in category entity_poly_seq in the ENTITY_POLY_SEQ category. The fraction of the atom type present at this site. The sum of the occupancies of all the atom types at this site may not significantly exceed 1.0 unless it is a dummy site. The estimated standard deviation of attribute occupancy in category atom_site. PDB atom name. PDB insertion code. PDB model number. PDB residue name. PDB residue number. PDB strand id. Author's alternate location identifier. Author's atom name. A concatenated series of single-letter codes which indicate the refinement restraints or constraints applied to this site. A description of restraints applied to specific parameters at this site during refinement. See also attribute refinement_flags in category atom_site and attribute ls_number_restraints in category refine. restrained to planar ring The multiplicity of a site due to the space-group symmetry as is given in International Tables for Crystallography, Vol. A (1987). A standard code used to describe the type of atomic displacement parameters used for the site. This data item is a pointer to attribute symbol in category atom_type in the ATOM_TYPE category. The value of attribute id in category atom_site must uniquely identify a record in the ATOM_SITE list. Note that this item need not be a number; it can be any unique identifier. This data item was introduced to facilitate compatibility between small molecule and macromolecular files. In the small molecule files, _atom_site_label is the identifier for the atom. In the macromolecular files, the atom identifier is the aggregate of _atom_site.label_alt_id, _atom_site.label_asym_id, _atom_site.label_atom_id, _atom_site.label_comp_id and attribute label_seq_id in category atom_site. For the two types of files to be compatible, a formal identifier for the category had to be introduced that was independent of the different modes of identifying atoms. For compatibility with older files, _atom_site_label is aliased to attribute id in category atom_site. 5 C12 Ca3g28 Fe3+17 H*251 boron2a C_a_phe_83_a_0 Zn_Zn_301_A_0 Data items in the ATOM_SITE_ANISOTROP category record details about temperature or thermal displacement factors, if those data items are contained in a separate list from the ATOM_SITE list. If the ATOM_SITE_ANISOTROP category is used for storing these data, the corresponding ATOM_SITE data items are not used. Example 1 - based on NDB structure BDL005 of Holbrook, Dickerson & Kim [(1985). Acta Cryst. B41, 255-262]. <PDBx:atom_site_anisotropCategory> <PDBx:atom_site_anisotrop id="1"> <PDBx:type_symbol>O</PDBx:type_symbol> <PDBx:U11>8642</PDBx:U11> <PDBx:U12>4866</PDBx:U12> <PDBx:U13>7299</PDBx:U13> <PDBx:U22>-342</PDBx:U22> <PDBx:U23>-258</PDBx:U23> <PDBx:U33>-1427</PDBx:U33> </PDBx:atom_site_anisotrop> <PDBx:atom_site_anisotrop id="2"> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:U11>5174</PDBx:U11> <PDBx:U12>4871</PDBx:U12> <PDBx:U13>6243</PDBx:U13> <PDBx:U22>-1885</PDBx:U22> <PDBx:U23>-2051</PDBx:U23> <PDBx:U33>-1377</PDBx:U33> </PDBx:atom_site_anisotrop> <PDBx:atom_site_anisotrop id="3"> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:U11>6202</PDBx:U11> <PDBx:U12>5020</PDBx:U12> <PDBx:U13>4395</PDBx:U13> <PDBx:U22>-1130</PDBx:U22> <PDBx:U23>-556</PDBx:U23> <PDBx:U33>-632</PDBx:U33> </PDBx:atom_site_anisotrop> <PDBx:atom_site_anisotrop id="4"> <PDBx:type_symbol>O</PDBx:type_symbol> <PDBx:U11>4224</PDBx:U11> <PDBx:U12>4700</PDBx:U12> <PDBx:U13>5046</PDBx:U13> <PDBx:U22>1105</PDBx:U22> <PDBx:U23>-161</PDBx:U23> <PDBx:U33>345</PDBx:U33> </PDBx:atom_site_anisotrop> <PDBx:atom_site_anisotrop id="5"> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:U11>8684</PDBx:U11> <PDBx:U12>4688</PDBx:U12> <PDBx:U13>4171</PDBx:U13> <PDBx:U22>-1850</PDBx:U22> <PDBx:U23>-433</PDBx:U23> <PDBx:U33>-292</PDBx:U33> </PDBx:atom_site_anisotrop> <PDBx:atom_site_anisotrop id="6"> <PDBx:type_symbol>O</PDBx:type_symbol> <PDBx:U11>11226</PDBx:U11> <PDBx:U12>5255</PDBx:U12> <PDBx:U13>3532</PDBx:U13> <PDBx:U22>-341</PDBx:U22> <PDBx:U23>2685</PDBx:U23> <PDBx:U33>1328</PDBx:U33> </PDBx:atom_site_anisotrop> <PDBx:atom_site_anisotrop id="7"> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:U11>10214</PDBx:U11> <PDBx:U12>2428</PDBx:U12> <PDBx:U13>5614</PDBx:U13> <PDBx:U22>-2610</PDBx:U22> <PDBx:U23>-1940</PDBx:U23> <PDBx:U33>902</PDBx:U33> </PDBx:atom_site_anisotrop> <PDBx:atom_site_anisotrop id="8"> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:U11>4590</PDBx:U11> <PDBx:U12>3488</PDBx:U12> <PDBx:U13>5827</PDBx:U13> <PDBx:U22>751</PDBx:U22> <PDBx:U23>-770</PDBx:U23> <PDBx:U33>986</PDBx:U33> </PDBx:atom_site_anisotrop> <PDBx:atom_site_anisotrop id="9"> <PDBx:type_symbol>N</PDBx:type_symbol> <PDBx:U11>5014</PDBx:U11> <PDBx:U12>4434</PDBx:U12> <PDBx:U13>3447</PDBx:U13> <PDBx:U22>-17</PDBx:U22> <PDBx:U23>-1593</PDBx:U23> <PDBx:U33>539</PDBx:U33> </PDBx:atom_site_anisotrop> </PDBx:atom_site_anisotropCategory> The [1][1] element of the anisotropic atomic displacement matrix B, which appears in the structure factor term as: T = exp{-1/4 sum~i~[sum~j~(B~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. The estimated standard deviation of attribute B[1][1] in category atom_site_anisotrop. The [1][2] element of the anisotropic atomic displacement matrix B, which appears in the structure factor term as: T = exp{-1/4 sum~i~[sum~j~(B~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. The estimated standard deviation of attribute B[1][2] in category atom_site_anisotrop. The [1][3] element of the anisotropic atomic displacement matrix B, which appears in the structure factor term as: T = exp{-1/4 sum~i~[sum~j~(B~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. The estimated standard deviation of attribute B[1][3] in category atom_site_anisotrop. The [2][2] element of the anisotropic atomic displacement matrix B, which appears in the structure factor term as: T = exp{-1/4 sum~i~[sum~j~(B~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. The estimated standard deviation of attribute B[2][2] in category atom_site_anisotrop. The [2][3] element of the anisotropic atomic displacement matrix B, which appears in the structure factor term as: T = exp{-1/4 sum~i~[sum~j~(B~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. The estimated standard deviation of attribute B[2][3] in category atom_site_anisotrop. The [3][3] element of the anisotropic atomic displacement matrix B, which appears in the structure factor term as: T = exp{-1/4 sum~i~[sum~j~(B~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. The estimated standard deviation of attribute B[3][3] in category atom_site_anisotrop. The [1][1] element of the standard anisotropic atomic displacement matrix U, which appears in the structure factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The estimated standard deviation of attribute U[1][1] in category atom_site_anisotrop. The [1][2] element of the standard anisotropic atomic displacement matrix U, which appears in the structure factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The estimated standard deviation of attribute U[1][2] in category atom_site_anisotrop. The [1][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The estimated standard deviation of attribute U[1][3] in category atom_site_anisotrop. The [2][2] element of the standard anisotropic atomic displacement matrix U, which appears in the structure factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The estimated standard deviation of attribute U[2][2] in category atom_site_anisotrop. The [2][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The estimated standard deviation of attribute U[2][3] in category atom_site_anisotrop. The [3][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The estimated standard deviation of attribute U[3][3] in category atom_site_anisotrop. Pointer to attribute pdbx_PDB_ins_code in category atom_site Pointer to attribute pdbx_auth_alt_id in category atom_site. Pointer to attribute auth_asym_id in category atom_site Pointer to attribute auth_atom_id in category atom_site Pointer to attribute auth_comp_id in category atom_site Pointer to attribute auth_seq_id in category atom_site Pointer to attribute label_alt_id in category atom_site. Pointer to attribute label_asym_id in category atom_site Pointer to attribute label_atom_id in category atom_site Pointer to attribute label_comp_id in category atom_site Pointer to attribute label_seq_id in category atom_site Ratio of the maximum to minimum principal axes of displacement (thermal) ellipsoids. This data item is a pointer to attribute symbol in category atom_type in the ATOM_TYPE category. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. Data items in the ATOM_SITES category record details about the crystallographic cell and cell transformations, which are common to all atom sites. Example 1 - based on PDB entry 5HVP and/or laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:atom_sitesCategory> <PDBx:atom_sites entry_id="5HVP"> <PDBx:Cartn_transform_axes>c along z, astar along x, b along y</PDBx:Cartn_transform_axes> <PDBx:Cartn_transf_matrix11>58.39</PDBx:Cartn_transf_matrix11> <PDBx:Cartn_transf_matrix12>0.00</PDBx:Cartn_transf_matrix12> <PDBx:Cartn_transf_matrix13>0.00</PDBx:Cartn_transf_matrix13> <PDBx:Cartn_transf_matrix21>0.00</PDBx:Cartn_transf_matrix21> <PDBx:Cartn_transf_matrix22>86.70</PDBx:Cartn_transf_matrix22> <PDBx:Cartn_transf_matrix23>0.00</PDBx:Cartn_transf_matrix23> <PDBx:Cartn_transf_matrix31>0.00</PDBx:Cartn_transf_matrix31> <PDBx:Cartn_transf_matrix32>0.00</PDBx:Cartn_transf_matrix32> <PDBx:Cartn_transf_matrix33>46.27</PDBx:Cartn_transf_matrix33> <PDBx:Cartn_transf_vector1>0.00</PDBx:Cartn_transf_vector1> <PDBx:Cartn_transf_vector2>0.00</PDBx:Cartn_transf_vector2> <PDBx:Cartn_transf_vector3>0.00</PDBx:Cartn_transf_vector3> </PDBx:atom_sites> </PDBx:atom_sitesCategory> The [1][1] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| The [1][2] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| The [1][3] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| The [2][1] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| The [2][2] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| The [2][3] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| The [3][1] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| The [3][2] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| The [3][3] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| The [1] element of the 3 element vector used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The rotation matrix is defined in attribute Cartn_transf_matrix[][]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| The [2] element of the 3 element vector used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The rotation matrix is defined in attribute Cartn_transf_matrix[][]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| The [3] element of the 3 element vector used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The rotation matrix is defined in attribute Cartn_transf_matrix[][]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| A description of the relative alignment of the crystal cell axes to the Cartesian orthogonal axes as applied in the transformation matrix attribute Cartn_transf_matrix in category atom_sites. a parallel to x; b in the plane of y & z The [1][1] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| The [1][2] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| The [1][3] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| The [2][1] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| The [2][3] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| The [2][3] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| The [3][1] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| The [3][2] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| The [3][3] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| The [1] element of the 3 element vector used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x3 rotation is defined in attribute fract_transf_matrix[][]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| The [2] element of the 3 element vector used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x3 rotation is defined in attribute fract_transf_matrix[][]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| The [3] element of the 3 element vector used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x3 rotation is defined in attribute fract_transf_matrix[][]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| A code which identifies the methods used to locate the initial atomic sites. The solution_hydrogens code identifies how the hydrogens were located. *** This data item would not in general be used in a macromolecular data block. *** A code which identifies the methods used to locate the initial atomic sites. The solution_primary code identifies how the first atom sites were determined. *** This data item would not in general be used in a macromolecular data block. *** A code which identifies the methods used to locate the initial atomic sites. The solution_secondary code identifies how the non-hydrogen sites not include in solution_primary were located. *** This data item would not in general be used in a macromolecular data block. *** This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the ATOM_SITES_ALT category record details about the structural ensembles that should be generated from atom sites or groups of atom sites that are modeled in alternative conformations in this data block. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:atom_sites_altCategory> <PDBx:atom_sites_alt id=""> <PDBx:details> Atom sites with the alternative id set to null are not modeled in alternative conformations</PDBx:details> </PDBx:atom_sites_alt> <PDBx:atom_sites_alt id="1"> <PDBx:details> Atom sites with the alternative id set to 1 have been modeled in alternative conformations with respect to atom sites marked with alternative id 2. The conformations of amino acid side chains and solvent atoms with alternative id set to 1 correlate with the conformation of the inhibitor marked with alternative id 1. They have been given an occupancy of 0.58 to match the occupancy assigned to the inhibitor.</PDBx:details> </PDBx:atom_sites_alt> <PDBx:atom_sites_alt id="2"> <PDBx:details> Atom sites with the alternative id set to 2 have been modeled in alternative conformations with respect to atom sites marked with alternative id 1. The conformations of amino acid side chains and solvent atoms with alternative id set to 2 correlate with the conformation of the inhibitor marked with alternative id 2. They have been given an occupancy of 0.42 to match the occupancy assigned to the inhibitor.</PDBx:details> </PDBx:atom_sites_alt> <PDBx:atom_sites_alt id="3"> <PDBx:details> Atom sites with the alternative id set to 3 have been modeled in alternative conformations with respect to atoms marked with alternative id 4. The conformations of amino acid side chains and solvent atoms with alternative id set to 3 do not correlate with the conformation of the inhibitor. These atom sites have arbitrarily been given an occupancy of 0.50.</PDBx:details> </PDBx:atom_sites_alt> <PDBx:atom_sites_alt id="4"> <PDBx:details> Atom sites with the alternative id set to 4 have been modeled in alternative conformations with respect to atoms marked with alternative id 3. The conformations of amino acid side chains and solvent atoms with alternative id set to 4 do not correlate with the conformation of the inhibitor. These atom sites have arbitrarily been given an occupancy of 0.50.</PDBx:details> </PDBx:atom_sites_alt> </PDBx:atom_sites_altCategory> A description of special aspects of the modeling of atoms in alternative conformations. The value of attribute id in category atom_sites_alt must uniquely identify a record in the ATOM_SITES_ALT list. Note that this item need not be a number; it can be any unique identifier. orientation 1 molecule abc Data items in the ATOM_SITES_ALT_ENS category record details about the ensemble structure generated from atoms with various alternative conformation ids. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:atom_sites_alt_ensCategory> <PDBx:atom_sites_alt_ens id="Ensemble 1-A"> <PDBx:details> The inhibitor binds to the enzyme in two, roughly twofold symmetric, alternative conformations. This conformational ensemble includes the more populated conformation of the inhibitor (id=1) and the amino acid side chains and solvent structure that correlate with this inhibitor conformation. Also included are one set (id=3) of side chains with alternative conformations when the conformations are not correlated with the inhibitor conformation.</PDBx:details> </PDBx:atom_sites_alt_ens> <PDBx:atom_sites_alt_ens id="Ensemble 1-B"> <PDBx:details> The inhibitor binds to the enzyme in two, roughly twofold symmetric alternative conformations. This conformational ensemble includes the more populated conformation of the inhibitor (id=1) and the amino acid side chains and solvent structure that correlate with this inhibitor conformation. Also included are one set (id=4) of side chains with alternative conformations when the conformations are not correlated with the inhibitor conformation.</PDBx:details> </PDBx:atom_sites_alt_ens> <PDBx:atom_sites_alt_ens id="Ensemble 2-A"> <PDBx:details> The inhibitor binds to the enzyme in two, roughly twofold symmetric alternative conformations. This conformational ensemble includes the less populated conformation of the inhibitor (id=2) and the amino acid side chains and solvent structure that correlate with this inhibitor conformation. Also included are one set (id=3) of side chains with alternative conformations when the conformations are not correlated with the inhibitor conformation.</PDBx:details> </PDBx:atom_sites_alt_ens> <PDBx:atom_sites_alt_ens id="Ensemble 2-B"> <PDBx:details> The inhibitor binds to the enzyme in two, roughly twofold symmetric alternative conformations. This conformational ensemble includes the less populated conformation of the inhibitor (id=2) and the amino acid side chains and solvent structure that correlate with this inhibitor conformation. Also included are one set (id=4) of side chains with alternative conformations when the conformations are not correlated with the inhibitor conformation.</PDBx:details> </PDBx:atom_sites_alt_ens> </PDBx:atom_sites_alt_ensCategory> A description of special aspects of the ensemble structure generated from atoms with various alternative ids. The value of attribute id in category atom_sites_alt_ens must uniquely identify a record in the ATOM_SITES_ALT_ENS list. Note that this item need not be a number; it can be any unique identifier. Data items in the ATOM_SITES_ALT_GEN category record details about the interpretation of multiple conformations in the structure. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:atom_sites_alt_genCategory> <PDBx:atom_sites_alt_gen ens_id="Ensemble 1-A" alt_id=""></PDBx:atom_sites_alt_gen> <PDBx:atom_sites_alt_gen ens_id="Ensemble 1-A" alt_id="1"></PDBx:atom_sites_alt_gen> <PDBx:atom_sites_alt_gen ens_id="Ensemble 1-A" alt_id="3"></PDBx:atom_sites_alt_gen> <PDBx:atom_sites_alt_gen ens_id="Ensemble 1-B" alt_id=""></PDBx:atom_sites_alt_gen> <PDBx:atom_sites_alt_gen ens_id="Ensemble 1-B" alt_id="1"></PDBx:atom_sites_alt_gen> <PDBx:atom_sites_alt_gen ens_id="Ensemble 1-B" alt_id="4"></PDBx:atom_sites_alt_gen> <PDBx:atom_sites_alt_gen ens_id="Ensemble 2-A" alt_id=""></PDBx:atom_sites_alt_gen> <PDBx:atom_sites_alt_gen ens_id="Ensemble 2-A" alt_id="2"></PDBx:atom_sites_alt_gen> <PDBx:atom_sites_alt_gen ens_id="Ensemble 2-A" alt_id="3"></PDBx:atom_sites_alt_gen> <PDBx:atom_sites_alt_gen ens_id="Ensemble 2-B" alt_id=""></PDBx:atom_sites_alt_gen> <PDBx:atom_sites_alt_gen ens_id="Ensemble 2-B" alt_id="2"></PDBx:atom_sites_alt_gen> <PDBx:atom_sites_alt_gen ens_id="Ensemble 2-B" alt_id="4"></PDBx:atom_sites_alt_gen> </PDBx:atom_sites_alt_genCategory> This data item is a pointer to attribute id in category atom_sites_alt_ens in the ATOM_SITES_ALT_ENS category. This data item is a pointer to attribute id in category atom_sites_alt in the ATOM_SITES_ALT category. Data items in the ATOM_SITES_FOOTNOTE category record detailed comments about an atom site or group of atom sites. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:atom_sites_footnoteCategory> <PDBx:atom_sites_footnote id="1"> <PDBx:text> The inhibitor binds to the enzyme in two alternative orientations. The two orientations have been assigned alternative ids *1* and *2*.</PDBx:text> </PDBx:atom_sites_footnote> <PDBx:atom_sites_footnote id="2"> <PDBx:text> Side chains of these residues adopt alternative orientations that correlate with the alternative orientations of the inhibitor. Side chains with alternative id *1* and occupancy 0.58 correlate with inhibitor orientation *1*. Side chains with alternative id *2* and occupancy 0.42 correlate with inhibitor orientation *2*.</PDBx:text> </PDBx:atom_sites_footnote> <PDBx:atom_sites_footnote id="3"> <PDBx:text> The positions of these water molecules correlate with the alternative orientations of the inhibitor. Water molecules with alternative id *1* and occupancy 0.58 correlate with inhibitor orientation *1*. Water molecules with alternative id *2* and occupancy 0.42 correlate with inhibitor orientation *2*.</PDBx:text> </PDBx:atom_sites_footnote> <PDBx:atom_sites_footnote id="4"> <PDBx:text> Side chains of these residues adopt alternative orientations that do not correlate with the alternative orientation of the inhibitor. </PDBx:text> </PDBx:atom_sites_footnote> <PDBx:atom_sites_footnote id="5"> <PDBx:text> The positions of these water molecules correlate with alternative orientations of amino acid side chains that do not correlate with alternative orientations of the inhibitor.</PDBx:text> </PDBx:atom_sites_footnote> </PDBx:atom_sites_footnoteCategory> The text of the footnote. Footnotes are used to describe an atom site or group of atom sites in the ATOM_SITE list. For example, footnotes may be used to indicate atoms for which the electron density is very weak, or atoms for which static disorder has been modeled, among many other possibilities. A code that identifies the footnote. a b 1 2 Data items in the ATOM_TYPE category record details about properties of the atoms that occupy the atom sites, such as the atomic scattering factors. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:atom_typeCategory> <PDBx:atom_type symbol="C"> <PDBx:oxidation_number>0</PDBx:oxidation_number> <PDBx:scat_Cromer_Mann_a1>2.31000</PDBx:scat_Cromer_Mann_a1> <PDBx:scat_Cromer_Mann_a2>20.8439</PDBx:scat_Cromer_Mann_a2> <PDBx:scat_Cromer_Mann_a3>1.02000</PDBx:scat_Cromer_Mann_a3> <PDBx:scat_Cromer_Mann_a4>10.2075</PDBx:scat_Cromer_Mann_a4> <PDBx:scat_Cromer_Mann_b1>1.58860</PDBx:scat_Cromer_Mann_b1> <PDBx:scat_Cromer_Mann_b2>0.568700</PDBx:scat_Cromer_Mann_b2> <PDBx:scat_Cromer_Mann_b3>0.865000</PDBx:scat_Cromer_Mann_b3> <PDBx:scat_Cromer_Mann_b4>51.6512</PDBx:scat_Cromer_Mann_b4> <PDBx:scat_Cromer_Mann_c>0.21560</PDBx:scat_Cromer_Mann_c> </PDBx:atom_type> <PDBx:atom_type symbol="N"> <PDBx:oxidation_number>0</PDBx:oxidation_number> <PDBx:scat_Cromer_Mann_a1>12.2126</PDBx:scat_Cromer_Mann_a1> <PDBx:scat_Cromer_Mann_a2>0.005700</PDBx:scat_Cromer_Mann_a2> <PDBx:scat_Cromer_Mann_a3>3.13220</PDBx:scat_Cromer_Mann_a3> <PDBx:scat_Cromer_Mann_a4>9.89330</PDBx:scat_Cromer_Mann_a4> <PDBx:scat_Cromer_Mann_b1>2.01250</PDBx:scat_Cromer_Mann_b1> <PDBx:scat_Cromer_Mann_b2>28.9975</PDBx:scat_Cromer_Mann_b2> <PDBx:scat_Cromer_Mann_b3>1.16630</PDBx:scat_Cromer_Mann_b3> <PDBx:scat_Cromer_Mann_b4>0.582600</PDBx:scat_Cromer_Mann_b4> <PDBx:scat_Cromer_Mann_c>-11.529</PDBx:scat_Cromer_Mann_c> </PDBx:atom_type> <PDBx:atom_type symbol="O"> <PDBx:oxidation_number>0</PDBx:oxidation_number> <PDBx:scat_Cromer_Mann_a1>3.04850</PDBx:scat_Cromer_Mann_a1> <PDBx:scat_Cromer_Mann_a2>13.2771</PDBx:scat_Cromer_Mann_a2> <PDBx:scat_Cromer_Mann_a3>2.28680</PDBx:scat_Cromer_Mann_a3> <PDBx:scat_Cromer_Mann_a4>5.70110</PDBx:scat_Cromer_Mann_a4> <PDBx:scat_Cromer_Mann_b1>1.54630</PDBx:scat_Cromer_Mann_b1> <PDBx:scat_Cromer_Mann_b2>0.323900</PDBx:scat_Cromer_Mann_b2> <PDBx:scat_Cromer_Mann_b3>0.867000</PDBx:scat_Cromer_Mann_b3> <PDBx:scat_Cromer_Mann_b4>32.9089</PDBx:scat_Cromer_Mann_b4> <PDBx:scat_Cromer_Mann_c>0.250800</PDBx:scat_Cromer_Mann_c> </PDBx:atom_type> <PDBx:atom_type symbol="S"> <PDBx:oxidation_number>0</PDBx:oxidation_number> <PDBx:scat_Cromer_Mann_a1>6.90530</PDBx:scat_Cromer_Mann_a1> <PDBx:scat_Cromer_Mann_a2>1.46790</PDBx:scat_Cromer_Mann_a2> <PDBx:scat_Cromer_Mann_a3>5.20340</PDBx:scat_Cromer_Mann_a3> <PDBx:scat_Cromer_Mann_a4>22.2151</PDBx:scat_Cromer_Mann_a4> <PDBx:scat_Cromer_Mann_b1>1.43790</PDBx:scat_Cromer_Mann_b1> <PDBx:scat_Cromer_Mann_b2>0.253600</PDBx:scat_Cromer_Mann_b2> <PDBx:scat_Cromer_Mann_b3>1.58630</PDBx:scat_Cromer_Mann_b3> <PDBx:scat_Cromer_Mann_b4>56.1720</PDBx:scat_Cromer_Mann_b4> <PDBx:scat_Cromer_Mann_c>0.866900</PDBx:scat_Cromer_Mann_c> </PDBx:atom_type> <PDBx:atom_type symbol="CL"> <PDBx:oxidation_number>-1</PDBx:oxidation_number> <PDBx:scat_Cromer_Mann_a1>18.2915</PDBx:scat_Cromer_Mann_a1> <PDBx:scat_Cromer_Mann_a2>0.006600</PDBx:scat_Cromer_Mann_a2> <PDBx:scat_Cromer_Mann_a3>7.20840</PDBx:scat_Cromer_Mann_a3> <PDBx:scat_Cromer_Mann_a4>1.17170</PDBx:scat_Cromer_Mann_a4> <PDBx:scat_Cromer_Mann_b1>6.53370</PDBx:scat_Cromer_Mann_b1> <PDBx:scat_Cromer_Mann_b2>19.5424</PDBx:scat_Cromer_Mann_b2> <PDBx:scat_Cromer_Mann_b3>2.33860</PDBx:scat_Cromer_Mann_b3> <PDBx:scat_Cromer_Mann_b4>60.4486</PDBx:scat_Cromer_Mann_b4> <PDBx:scat_Cromer_Mann_c>-16.378</PDBx:scat_Cromer_Mann_c> </PDBx:atom_type> </PDBx:atom_typeCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. <PDBx:atom_typeCategory> <PDBx:atom_type symbol="C"> <PDBx:oxidation_number>0</PDBx:oxidation_number> <PDBx:number_in_cell>72</PDBx:number_in_cell> <PDBx:scat_dispersion_real>.017</PDBx:scat_dispersion_real> <PDBx:scat_dispersion_imag>.009</PDBx:scat_dispersion_imag> <PDBx:scat_source>International_Tables_Vol_IV_Table_2.2B</PDBx:scat_source> </PDBx:atom_type> <PDBx:atom_type symbol="H"> <PDBx:oxidation_number>0</PDBx:oxidation_number> <PDBx:number_in_cell>100</PDBx:number_in_cell> <PDBx:scat_dispersion_real>0</PDBx:scat_dispersion_real> <PDBx:scat_dispersion_imag>0</PDBx:scat_dispersion_imag> <PDBx:scat_source>International_Tables_Vol_IV_Table_2.2B</PDBx:scat_source> </PDBx:atom_type> <PDBx:atom_type symbol="O"> <PDBx:oxidation_number>0</PDBx:oxidation_number> <PDBx:number_in_cell>12</PDBx:number_in_cell> <PDBx:scat_dispersion_real>.047</PDBx:scat_dispersion_real> <PDBx:scat_dispersion_imag>.032</PDBx:scat_dispersion_imag> <PDBx:scat_source>International_Tables_Vol_IV_Table_2.2B</PDBx:scat_source> </PDBx:atom_type> <PDBx:atom_type symbol="N"> <PDBx:oxidation_number>0</PDBx:oxidation_number> <PDBx:number_in_cell>4</PDBx:number_in_cell> <PDBx:scat_dispersion_real>.029</PDBx:scat_dispersion_real> <PDBx:scat_dispersion_imag>.018</PDBx:scat_dispersion_imag> <PDBx:scat_source>International_Tables_Vol_IV_Table_2.2B</PDBx:scat_source> </PDBx:atom_type> </PDBx:atom_typeCategory> Mass percentage of this atom type derived from chemical analysis. A description of the atom(s) designated by this atom type. In most cases this is the element name and oxidation state of a single atom species. For disordered or nonstoichiometric structures it will describe a combination of atom species. deuterium 0.34Fe+0.66Ni Total number of atoms of this atom type in the unit cell. Formal oxidation state of this atom type in the structure. The effective intramolecular bonding radius in angstroms of this atom type. The effective intermolecular bonding radius in angstroms of this atom type. The a1 Cromer-Mann scattering-factor coefficient used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography, Vol. IV, (1974). Table 2.2B. or: International Tables for Crystallography, Vol. C, (1991). Tables 6.1.1.4 and 6.1.1.5. The a2 Cromer-Mann scattering-factor coefficient used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography, Vol. IV, (1974). Table 2.2B. or: International Tables for Crystallography, Vol. C, (1991). Tables 6.1.1.4 and 6.1.1.5. The a3 Cromer-Mann scattering-factor coefficient used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography, Vol. IV, (1974). Table 2.2B. or: International Tables for Crystallography, Vol. C, (1991). Tables 6.1.1.4 and 6.1.1.5. The a4 Cromer-Mann scattering-factor coefficient used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography, Vol. IV, (1974). Table 2.2B. or: International Tables for Crystallography, Vol. C, (1991). Tables 6.1.1.4 and 6.1.1.5. The b1 Cromer-Mann scattering-factor coefficient used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography, Vol. IV, (1974). Table 2.2B. or: International Tables for Crystallography, Vol. C, (1991). Tables 6.1.1.4 and 6.1.1.5. The b2 Cromer-Mann scattering-factor coefficient used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography, Vol. IV, (1974). Table 2.2B. or: International Tables for Crystallography, Vol. C, (1991). Tables 6.1.1.4 and 6.1.1.5. The b3 Cromer-Mann scattering-factor coefficient used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography, Vol. IV, (1974). Table 2.2B. or: International Tables for Crystallography, Vol. C, (1991). Tables 6.1.1.4 and 6.1.1.5. The b4 Cromer-Mann scattering-factor coefficient used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography, Vol. IV, (1974). Table 2.2B. or: International Tables for Crystallography, Vol. C, (1991). Tables 6.1.1.4 and 6.1.1.5. The c Cromer-Mann scattering-factor coefficient used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography, Vol. IV, (1974). Table 2.2B. or: International Tables for Crystallography, Vol. C, (1991). Tables 6.1.1.4 and 6.1.1.5. The imaginary component of the anomalous dispersion scattering factors, f'' (in electrons), for this atom type and the radiation identified by attribute id in category diffrn_radiation_wavelength. The real component of the anomalous dispersion scattering factors, f' (in electrons), for this atom type and the radiation identified by attribute id in category diffrn_radiation_wavelength. The bound coherent scattering length in femtometres for the atom type at the isotopic composition used for the diffraction experiment. Reference to source of scattering factors used for this atom type. International Tables Vol IV Table 2.4.6B A table of scattering factors as a function of sin theta over lambda. This table should be well commented to indicate the items present. Regularly formatted lists are strongly recommended. The code used to identify the atom specie(s) representing this atom type. Normally this code is the element symbol. The code may be composed of any character except an underline with the additional proviso that digits designate an oxidation state and must be followed by a + or - character. C Cu2+ H(SDS) dummy FeNi Data items in the AUDIT category record details about the creation and subsequent updating of the data block. Note that these items apply only to the creation and updating of the data block, and should not be confused with the data items (in the JOURNAL category) that describe the time course of publication of the material in the data block. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:auditCategory> <PDBx:audit revision_id="1"> <PDBx:creation_date>1992-12-08</PDBx:creation_date> <PDBx:creation_method> Created by hand from PDB entry 5HVP, from the J. Biol. Chem. paper describing this structure and from laboratory records</PDBx:creation_method> <PDBx:update_record> 1992-12-09 adjusted to reflect comments from Brian McKeever 1992-12-10 adjusted to reflect comments from Helen Berman 1992-12-12 adjusted to reflect comments from Keith Watenpaugh</PDBx:update_record> </PDBx:audit> </PDBx:auditCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. <PDBx:auditCategory> <PDBx:audit> <PDBx:creation_date>1991-03-20</PDBx:creation_date> <PDBx:creation_method>from_xtal_archive_file_using_CIFIO</PDBx:creation_method> <PDBx:update_record> 1991-04-09 text and data added by Tony Willis. 1991-04-15 rec&apos;d by co-editor with diagram as manuscript HL7. 1991-04-17 adjustments based on first referees report. 1991-04-18 adjustments based on second referees report.</PDBx:update_record> </PDBx:audit> </PDBx:auditCategory> A date that the data block was created. The date format is yyyy-mm-dd. 1990-07-12 A description of how data were entered into the data block. spawned by the program QBEE A record of any changes to the data block. The update format is a date (yyyy-mm-dd) followed by a description of the changes. The latest update entry is added to the bottom of this record. 1990-07-15 Updated by the Co-editor The value of attribute revision_id in category audit must uniquely identify a record in the AUDIT list. rev1 Data items in the AUDIT_AUTHOR category record details about the author(s) of the data block. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:audit_authorCategory> <PDBx:audit_author name="Fitzgerald, Paula M.D."> <PDBx:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</PDBx:address> </PDBx:audit_author> <PDBx:audit_author name="McKeever, Brian M."> <PDBx:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</PDBx:address> </PDBx:audit_author> <PDBx:audit_author name="Van Middlesworth, J.F."> <PDBx:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</PDBx:address> </PDBx:audit_author> <PDBx:audit_author name="Springer, James P."> <PDBx:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</PDBx:address> </PDBx:audit_author> </PDBx:audit_authorCategory> The address of an author of this data block. If there are multiple authors, attribute address in category audit_author is looped with attribute name in category audit_author. Department Institute Street City and postcode COUNTRY The name of an author of this data block. If there are multiple authors, _audit_author.name is looped with _audit_author.address. The family name(s), followed by a comma and including any dynastic compoents, precedes the first name(s) or initial(s). Bleary, Percival R. O'Neil, F.K. Van den Bossche, G. Yang, D.-L. Simonov, Yu.A Data items in the AUDIT_CONFORM category describe the dictionary versions against which the data names appearing in the current data block are conformant. Example 1 - Any file conforming to the current CIF core dictionary. <PDBx:audit_conformCategory> <PDBx:audit_conform dict_name="cif_core.dic" dict_version="2.0"> <PDBx:dict_location>ftp://ftp.iucr.ac.uk/pub/cifdic.c96</PDBx:dict_location> </PDBx:audit_conform> </PDBx:audit_conformCategory> A file name or uniform resource locator (URL) where the conformant dictionary resides. The string identifying the highest-level dictionary defining datanames used in this file. The version number of the conformant dictionary. Data items in the AUDIT_CONTACT_AUTHOR category record details about the name and address of the author to be contacted concerning the contents of this data block. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:audit_contact_authorCategory> <PDBx:audit_contact_author name="Fitzgerald, Paula M.D."> <PDBx:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</PDBx:address> <PDBx:phone>908 594 5510</PDBx:phone> <PDBx:fax>908 594 6645</PDBx:fax> <PDBx:email>paula_fitzgerald@merck.com</PDBx:email> </PDBx:audit_contact_author> </PDBx:audit_contact_authorCategory> The mailing address of the author of the data block to whom correspondence should be addressed. Department Institute Street City and postcode COUNTRY The electronic mail address of the author of the data block to whom correspondence should be addressed, in a form recognisable to international networks. name@host.domain.country bm@iucr.ac.uk The facsimile telephone number of the author of the data block to whom correspondence should be addressed. The recommended style includes the international dialing prefix, the area code in parentheses, followed by the local number with no spaces. The earlier convention of including the international dialing prefixes in parentheses is no longer recommended. 12(34)9477334 12()349477334 The telephone number of the author of the data block to whom correspondence should be addressed. The recommended style includes the international dialing prefix, the area code in parentheses, followed by the local number and any extension number prefixed by 'x', with no spaces. The earlier convention of including the international dialing prefixes in parentheses is no longer recommended. 12(34)9477330 12()349477330 12(34)9477330x5543 The name of the author of the data block to whom correspondence should be addressed. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s). Bleary, Percival R. O'Neil, F.K. Van den Bossche, G. Yang, D.-L. Simonov, Yu.A Data items in the CELL category record details about the crystallographic cell parameters. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:cellCategory> <PDBx:cell entry_id="5HVP"> <PDBx:length_a>58.39</PDBx:length_a> <PDBx:length_a_esd>0.05</PDBx:length_a_esd> <PDBx:length_b>86.70</PDBx:length_b> <PDBx:length_b_esd>0.12</PDBx:length_b_esd> <PDBx:length_c>46.27</PDBx:length_c> <PDBx:length_c_esd>0.06</PDBx:length_c_esd> <PDBx:angle_alpha>90.00</PDBx:angle_alpha> <PDBx:angle_beta>90.00</PDBx:angle_beta> <PDBx:angle_gamma>90.00</PDBx:angle_gamma> <PDBx:volume>234237</PDBx:volume> <PDBx:details> The cell parameters were refined every twenty frames during data integration. The cell lengths given are the mean of 55 such refinements; the esds given are the root mean square deviations of these 55 observations from that mean.</PDBx:details> </PDBx:cell> </PDBx:cellCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. <PDBx:cellCategory> <PDBx:cell> <PDBx:length_a>5.959</PDBx:length_a> <PDBx:length_a_esd>0.001</PDBx:length_a_esd> <PDBx:length_b>14.956</PDBx:length_b> <PDBx:length_b_esd>0.001</PDBx:length_b_esd> <PDBx:length_c>19.737</PDBx:length_c> <PDBx:length_c_esd>0.003</PDBx:length_c_esd> <PDBx:angle_alpha>90.0</PDBx:angle_alpha> <PDBx:angle_beta>90.0</PDBx:angle_beta> <PDBx:angle_gamma>90.0</PDBx:angle_gamma> <PDBx:volume>1759.0</PDBx:volume> <PDBx:volume_esd>0.3</PDBx:volume_esd> </PDBx:cell> </PDBx:cellCategory> The number of the polymeric chains in a unit cell. In the case of heteropolymers, Z is the number of occurrences of the most populous chain. This data item is provided for compatibility with the original Protein Data Bank format, and only for that purpose. Unit-cell angle alpha in degrees of the reported structure. The estimated standard deviation of attribute angle_alpha in category cell. Unit-cell angle beta in degrees of the reported structure. The estimated standard deviation of attribute angle_beta in category cell. Unit-cell angle gamma in degrees of the reported structure. The estimated standard deviation of attribute angle_gamma in category cell. A description of special aspects of the cell choice, noting possible alternative settings. pseudo-orthorhombic standard setting from 45 deg rotation around c The number of the formula units in the unit cell as specified by _chemical_formula.structural, _chemical_formula.moiety or attribute sum in category chemical_formula. Unit-cell length a corresponding to the structure reported. The estimated standard deviation of attribute length_a in category cell. Unit-cell length b corresponding to the structure reported. The estimated standard deviation of attribute length_b in category cell. Unit-cell length c corresponding to the structure reported. The estimated standard deviation of attribute length_c in category cell. To further identify unique axis if necessary. E.g., P 21 with an unique C axis will have 'C' in this field. Cell volume V in angstroms cubed. V = a b c (1 - cos^2^~alpha~ - cos^2^~beta~ - cos^2^~gamma~ + 2 cos~alpha~ cos~beta~ cos~gamma~)^1/2^ a = attribute length_a in category cell b = attribute length_b in category cell c = attribute length_c in category cell alpha = attribute angle_alpha in category cell beta = attribute angle_beta in category cell gamma = attribute angle_gamma in category cell The estimated standard deviation of attribute volume in category cell. This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the CELL_MEASUREMENT category record details about the measurement of the crystallographic cell parameters. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:cell_measurementCategory> <PDBx:cell_measurement entry_id="5HVP"> <PDBx:temp>293</PDBx:temp> <PDBx:temp_esd>3</PDBx:temp_esd> <PDBx:theta_min>11</PDBx:theta_min> <PDBx:theta_max>31</PDBx:theta_max> <PDBx:wavelength>1.54</PDBx:wavelength> </PDBx:cell_measurement> </PDBx:cell_measurementCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. <PDBx:cell_measurementCategory> <PDBx:cell_measurement> <PDBx:temp>293</PDBx:temp> <PDBx:reflns_used>25</PDBx:reflns_used> <PDBx:theta_min>25</PDBx:theta_min> <PDBx:theta_max>31</PDBx:theta_max> </PDBx:cell_measurement> </PDBx:cell_measurementCategory> The pressure in kilopascals at which the unit-cell parameters were measured (not the pressure used to synthesize the sample). The estimated standard deviation of attribute pressure in category cell_measurement. Description of the radiation used to measure the unit-cell data. See also attribute wavelength in category cell_measurement. neutron Cu K\a synchrotron The total number of reflections used to determine the unit cell. These reflections may be specified as CELL_MEASUREMENT_REFLN data items. The temperature in kelvins at which the unit-cell parameters were measured (not the temperature of synthesis). The estimated standard deviation of attribute temp in category cell_measurement. The maximum theta angle in degrees of reflections used to measure the unit cell. The minimum theta angle in degrees of reflections used to measure the unit cell. The wavelength in angstroms of the radiation used to measure the unit cell. If this is not specified, the wavelength is assumed to be that specified in the category DIFFRN_RADIATION_WAVELENGTH. This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the CELL_MEASUREMENT_REFLN category record details about the reflections used in determination of the crystallographic cell parameters. The CELL_MEASUREMENT_REFLN data items would in general be used only for diffractometer data. Example 1 - extracted from the CAD-4 listing of Rb~2~S~2~O~6~ at room temperature (not yet published). <PDBx:cell_measurement_reflnCategory> <PDBx:cell_measurement_refln index_h="-2" index_k="4" index_l="1"> <PDBx:theta>8.67</PDBx:theta> </PDBx:cell_measurement_refln> <PDBx:cell_measurement_refln index_h="0" index_k="3" index_l="2"> <PDBx:theta>9.45</PDBx:theta> </PDBx:cell_measurement_refln> <PDBx:cell_measurement_refln index_h="3" index_k="0" index_l="2"> <PDBx:theta>9.46</PDBx:theta> </PDBx:cell_measurement_refln> <PDBx:cell_measurement_refln index_h="-3" index_k="4" index_l="1"> <PDBx:theta>8.93</PDBx:theta> </PDBx:cell_measurement_refln> <PDBx:cell_measurement_refln index_h="-2" index_k="1" index_l="-2"> <PDBx:theta>7.53</PDBx:theta> </PDBx:cell_measurement_refln> <PDBx:cell_measurement_refln index_h="10" index_k="0" index_l="0"> <PDBx:theta>23.77</PDBx:theta> </PDBx:cell_measurement_refln> <PDBx:cell_measurement_refln index_h="0" index_k="10" index_l="0"> <PDBx:theta>23.78</PDBx:theta> </PDBx:cell_measurement_refln> <PDBx:cell_measurement_refln index_h="-5" index_k="4" index_l="1"> <PDBx:theta>11.14</PDBx:theta> </PDBx:cell_measurement_refln> </PDBx:cell_measurement_reflnCategory> Theta angle in degrees of a reflection used for measurement of the unit cell. Miller index h of a reflection used for measurement of the unit cell. Miller index k of a reflection used for measurement of the unit cell. Miller index l of a reflection used for measurement of the unit cell. Data items in the CHEM_COMP category give details (such as name, mass, charge, etc.) about each of the chemical components from which the relevant chemical structures can be constructed. The related categories CHEM_COMP_ATOM, CHEM_COMP_BOND, CHEM_COMP_ANGLE, etc. describe the detailed geometry of these chemical components. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:chem_compCategory> <PDBx:chem_comp id="phe"> <PDBx:model_source>1987 Protin/Prolsq Ideals file</PDBx:model_source> <PDBx:name>phenylalanine</PDBx:name> </PDBx:chem_comp> <PDBx:chem_comp id="val"> <PDBx:model_source>1987 Protin/Prolsq Ideals file</PDBx:model_source> <PDBx:name>alanine</PDBx:name> </PDBx:chem_comp> </PDBx:chem_compCategory> The formula for the chemical component. Formulae are written according to the rules: 1. Only recognised element symbols may be used. 2. Each element symbol is followed by a 'count' number. A count of '1' may be omitted. 3. A space or parenthesis must separate each element symbol and its count, but in general parentheses are not used. 4. The order of elements depends on whether or not carbon is present. If carbon is present, the order should be: C, then H, then the other elements in alphabetical order of their symbol. If carbon is not present, the elements are listed purely in alphabetic order of their symbol. This is the 'Hill' system used by Chemical Abstracts. C18 H19 N7 O8 S Formula mass in daltons of the chemical component. A description of special aspects of the generation of the coordinates for the model of the component. geometry idealized but not minimized A pointer to an 'external reference file', if the atomic description of the component is taken from such a file. The source of the coordinates for the model of the component. CSD entry ABCDEF built using Quanta/Charmm A description of the class of a non-standard monomer, if the group represents a modification of a standard monomer. iodinated base phosphorylated amino acid brominated base modified amino acid glycosylated amino acid A description of special details of a non-standard monomer. 'yes' indicates that this is a "standard" monomer, 'no' that it is "non-standard." Non-standard monomers should be further described using the attribute mon_nstd_parent, in category chem_comp _chem_comp.mon_nstd_class, and _chem_comp.mon_nstd_details data items. A name of the parent monomer of the non-standard monomer, if this group represents a modification of a standard monomer. tyrosine cytosine The identifier for the parent component of the non-standard component. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. The full name of the component. alanine valine adenine cytosine The total number of atoms in the component. The number of non-hydrogen atoms in the component. For standard polymer components, the one-letter code for the component. If there is not a standard one-letter code for this component, or if this is a non-polymer component, the one-letter code should be given as 'X'. This code may be preceded by a '+' character to indicate that the component is a modification of a standard component. alanine or adenine A ambiguous asparagine/aspartic-acid B arginine R asparagine N aspartic-acid D cysteine or cystine or cytosine C glutamine Q glutamic-acid E ambiguous glutamine/glutamic acid Z glycine or guanine G histidine H isoleucine I leucine L lysine K methionine M phenylalanine F proline P serine S threonine or thymine T tryptophan W tyrosine Y valine V uracil U water O other X Atom name alignment offset in PDB atom field. A serial number used by PDB in the FORMUL record. 3 The net integer charge assigned to this component. This is the formal charge assignment normally found in chemical diagrams. For nonstandard components a text description of modification of the parent component. ATP Synonym list for the component. ATP A preliminary classification used by PDB. For standard polymer components, the three-letter code for the component. If there is not a standard three-letter code for this component, or if this is a non-polymer component, the three-letter code should be given as 'UNK'. This code may be preceded by a '+' character to indicate that the component is a modification of a standard component. alanine ALA arginine ARG asparagine ASN aspartic-acid ASP ambiguous asparagine/aspartic-acid ASX cysteine CYS glutamine GLN glutamic-acid GLU glycine GLY ambiguous glutamine/glutamic acid GLX histidine HIS isoleucine ILE leucine LEU lysine LYS methionine MET phenylalanine PHE proline PRO serine SER threonine THR tryptophan TRP tyrosine TRY valine VAL 1-methyladenosine 1MA 5-methycytosine 5MC 2(prime)-O-methycytodine OMC 1-methyguanosine 1MG N(2)-methyguanosine 2MG N(2)-dimethyguanosine M2G 7-methyguanosine 7MG 2(prime)-O-methyguanosine 0MG diydrouridine H2U ribosylthymidine 5MU pseudouridine PSU acetic acid ACE formic acid FOR water HOH other UNK For standard polymer components, the type of the monomer. Note that monomers that will form polymers are of three types: linking monomers, monomers with some type of N-terminal (or 5') cap, and monomers with some type of C-terminal (or 3') cap. The value of attribute id in category chem_comp must uniquely identify each item in the CHEM_COMP list. For protein polymer entities, this is the three-letter code for amino acids. For nucleic acid polymer entities, this is the one-letter code for the bases. ala val A C Data items in the CHEM_COMP_ANGLE category record details about angles in a chemical component. Angles are designated by three atoms, with the second atom forming the vertex of the angle. Target values may be specified as angles in degrees, as a distance between the first and third atoms, or both. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:chem_comp_angleCategory> <PDBx:chem_comp_angle comp_id="phe" atom_id_1="N" atom_id_2="CA" atom_id_3="C"> <PDBx:value_angle>xxx.xx</PDBx:value_angle> <PDBx:value_dist>x.xx</PDBx:value_dist> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle comp_id="phe" atom_id_1="CA" atom_id_2="C" atom_id_3="O"> <PDBx:value_angle>xxx.xx</PDBx:value_angle> <PDBx:value_dist>x.xx</PDBx:value_dist> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle comp_id="phe" atom_id_1="CB" atom_id_2="CA" atom_id_3="C"> <PDBx:value_angle>xxx.xx</PDBx:value_angle> <PDBx:value_dist>x.xx</PDBx:value_dist> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle comp_id="phe" atom_id_1="CB" atom_id_2="CA" atom_id_3="N"> <PDBx:value_angle>xxx.xx</PDBx:value_angle> <PDBx:value_dist>x.xx</PDBx:value_dist> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle comp_id="phe" atom_id_1="CA" atom_id_2="CB" atom_id_3="CG"> <PDBx:value_angle>xxx.xx</PDBx:value_angle> <PDBx:value_dist>x.xx</PDBx:value_dist> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle comp_id="phe" atom_id_1="CB" atom_id_2="CG" atom_id_3="CD1"> <PDBx:value_angle>xxx.xx</PDBx:value_angle> <PDBx:value_dist>x.xx</PDBx:value_dist> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle comp_id="phe" atom_id_1="CB" atom_id_2="CG" atom_id_3="CD2"> <PDBx:value_angle>xxx.xx</PDBx:value_angle> <PDBx:value_dist>x.xx</PDBx:value_dist> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle comp_id="phe" atom_id_1="CD1" atom_id_2="CG" atom_id_3="CD2"> <PDBx:value_angle>xxx.xx</PDBx:value_angle> <PDBx:value_dist>x.xx</PDBx:value_dist> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle comp_id="phe" atom_id_1="CG" atom_id_2="CD1" atom_id_3="CE1"> <PDBx:value_angle>xxx.xx</PDBx:value_angle> <PDBx:value_dist>x.xx</PDBx:value_dist> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle comp_id="phe" atom_id_1="CD1" atom_id_2="CE1" atom_id_3="CZ"> <PDBx:value_angle>xxx.xx</PDBx:value_angle> <PDBx:value_dist>x.xx</PDBx:value_dist> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle comp_id="phe" atom_id_1="CE1" atom_id_2="CZ" atom_id_3="CE2"> <PDBx:value_angle>xxx.xx</PDBx:value_angle> <PDBx:value_dist>x.xx</PDBx:value_dist> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle comp_id="phe" atom_id_1="CZ" atom_id_2="CE2" atom_id_3="CD2"> <PDBx:value_angle>xxx.xx</PDBx:value_angle> <PDBx:value_dist>x.xx</PDBx:value_dist> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle comp_id="phe" atom_id_1="CG" atom_id_2="CD2" atom_id_3="CE2"> <PDBx:value_angle>xxx.xx</PDBx:value_angle> <PDBx:value_dist>x.xx</PDBx:value_dist> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle comp_id="val" atom_id_1="N" atom_id_2="CA" atom_id_3="C"> <PDBx:value_angle>xxx.xx</PDBx:value_angle> <PDBx:value_dist>x.xx</PDBx:value_dist> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle comp_id="val" atom_id_1="CA" atom_id_2="C" atom_id_3="O"> <PDBx:value_angle>xxx.xx</PDBx:value_angle> <PDBx:value_dist>x.xx</PDBx:value_dist> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle comp_id="val" atom_id_1="CB" atom_id_2="CA" atom_id_3="C"> <PDBx:value_angle>xxx.xx</PDBx:value_angle> <PDBx:value_dist>x.xx</PDBx:value_dist> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle comp_id="val" atom_id_1="CB" atom_id_2="CA" atom_id_3="N"> <PDBx:value_angle>xxx.xx</PDBx:value_angle> <PDBx:value_dist>x.xx</PDBx:value_dist> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle comp_id="val" atom_id_1="CA" atom_id_2="CB" atom_id_3="CG1"> <PDBx:value_angle>xxx.xx</PDBx:value_angle> <PDBx:value_dist>x.xx</PDBx:value_dist> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle comp_id="val" atom_id_1="CA" atom_id_2="CB" atom_id_3="CG2"> <PDBx:value_angle>xxx.xx</PDBx:value_angle> <PDBx:value_dist>x.xx</PDBx:value_dist> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle comp_id="val" atom_id_1="CG1" atom_id_2="CB" atom_id_3="CG2"> <PDBx:value_angle>xxx.xx</PDBx:value_angle> <PDBx:value_dist>x.xx</PDBx:value_dist> </PDBx:chem_comp_angle> </PDBx:chem_comp_angleCategory> The value that should be taken as the target value for the angle associated with the specified atoms, expressed in degrees. The estimated standard deviation of attribute value_angle in category chem_comp_angle. The value that should be taken as the target value for the angle associated with the specified atoms, expressed as the distance between the atoms specified by attribute atom_id_1 in category chem_comp_angle and attribute atom_id_3 in category chem_comp_angle. The estimated standard deviation of attribute value_dist_esd in category chem_comp_angle. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. The id of the first of the three atoms that define the angle. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. The id of the second of the three atoms that define the angle. The second atom is taken to be the apex of the angle. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. The id of the third of the three atoms that define the angle. This data item is a pointer to attribute atom_id in category chem_comp_atom in the chem_comp_atom category. Data items in the CHEM_COMP_ATOM category record details about the atoms in a chemical component. Atomic coordinates can be given for the components; specifying coordinates is an alternative to specifying the structure of the component via bonds, angles, planes, etc., in the appropriate CHEM_COMP subcategories. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:chem_comp_atomCategory> <PDBx:chem_comp_atom comp_id="phe" atom_id="N"> <PDBx:type_symbol>N</PDBx:type_symbol> <PDBx:substruct_code>main</PDBx:substruct_code> <PDBx:model_Cartn_x>1.20134</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.84658</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>0.00000</PDBx:model_Cartn_z> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom comp_id="phe" atom_id="CA"> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:substruct_code>main</PDBx:substruct_code> <PDBx:model_Cartn_x>0.00000</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.00000</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>0.00000</PDBx:model_Cartn_z> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom comp_id="phe" atom_id="C"> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:substruct_code>main</PDBx:substruct_code> <PDBx:model_Cartn_x>-1.25029</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.88107</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>0.00000</PDBx:model_Cartn_z> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom comp_id="phe" atom_id="O"> <PDBx:type_symbol>O</PDBx:type_symbol> <PDBx:substruct_code>main</PDBx:substruct_code> <PDBx:model_Cartn_x>-2.18525</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.66029</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>-0.78409</PDBx:model_Cartn_z> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom comp_id="phe" atom_id="CB"> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:substruct_code>side</PDBx:substruct_code> <PDBx:model_Cartn_x>0.00662</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>-1.03603</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>1.11081</PDBx:model_Cartn_z> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom comp_id="phe" atom_id="CG"> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:substruct_code>side</PDBx:substruct_code> <PDBx:model_Cartn_x>0.03254</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>-0.49711</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>2.50951</PDBx:model_Cartn_z> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom comp_id="phe" atom_id="CD1"> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:substruct_code>side</PDBx:substruct_code> <PDBx:model_Cartn_x>-1.15813</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>-0.12084</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>3.13467</PDBx:model_Cartn_z> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom comp_id="phe" atom_id="CE1"> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:substruct_code>side</PDBx:substruct_code> <PDBx:model_Cartn_x>-1.15720</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.38038</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>4.42732</PDBx:model_Cartn_z> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom comp_id="phe" atom_id="CZ"> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:substruct_code>side</PDBx:substruct_code> <PDBx:model_Cartn_x>0.05385</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.51332</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>5.11032</PDBx:model_Cartn_z> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom comp_id="phe" atom_id="CE2"> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:substruct_code>side</PDBx:substruct_code> <PDBx:model_Cartn_x>1.26137</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.11613</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>4.50975</PDBx:model_Cartn_z> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom comp_id="phe" atom_id="CD2"> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:substruct_code>side</PDBx:substruct_code> <PDBx:model_Cartn_x>1.23668</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>-0.38351</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>3.20288</PDBx:model_Cartn_z> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom comp_id="val" atom_id="N"> <PDBx:type_symbol>N</PDBx:type_symbol> <PDBx:substruct_code>main</PDBx:substruct_code> <PDBx:model_Cartn_x>1.20134</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.84658</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>0.00000</PDBx:model_Cartn_z> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom comp_id="val" atom_id="CA"> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:substruct_code>main</PDBx:substruct_code> <PDBx:model_Cartn_x>0.00000</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.00000</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>0.00000</PDBx:model_Cartn_z> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom comp_id="val" atom_id="C"> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:substruct_code>main</PDBx:substruct_code> <PDBx:model_Cartn_x>-1.25029</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.88107</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>0.00000</PDBx:model_Cartn_z> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom comp_id="val" atom_id="O"> <PDBx:type_symbol>O</PDBx:type_symbol> <PDBx:substruct_code>main</PDBx:substruct_code> <PDBx:model_Cartn_x>-2.18525</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.66029</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>-0.78409</PDBx:model_Cartn_z> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom comp_id="val" atom_id="CB"> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:substruct_code>side</PDBx:substruct_code> <PDBx:model_Cartn_x>0.05260</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>-0.99339</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>1.17429</PDBx:model_Cartn_z> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom comp_id="val" atom_id="CG1"> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:substruct_code>side</PDBx:substruct_code> <PDBx:model_Cartn_x>-0.13288</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>-0.31545</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>2.52668</PDBx:model_Cartn_z> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom comp_id="val" atom_id="CG2"> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:substruct_code>side</PDBx:substruct_code> <PDBx:model_Cartn_x>-0.94265</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>-2.12930</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>0.99811</PDBx:model_Cartn_z> </PDBx:chem_comp_atom> </PDBx:chem_comp_atomCategory> An alternative identifier for the atom. This data item would be used in cases where alternative nomenclatures exist for labeling atoms in a group. The net integer charge assigned to this atom. This is the formal charge assignment normally found in chemical diagrams. for an ammonium nitrogen 1 for a chloride ion -1 The x component of the coordinates for this atom in this component specified as orthogonal angstroms. The choice of reference axis frame for the coordinates is arbitrary. The set of coordinates input for the entity here is intended to correspond to the atomic model used to generate restraints for structure refinement, and not to atom sites in the _atom_site list. The estimated standard deviation of attribute model_Cartn_x in category chem_comp_atom. The y component of the coordinates for this atom in this component specified as orthogonal angstroms. The choice of reference axis frame for the coordinates is arbitrary. The set of coordinates input for the entity here is intended to correspond to the atomic model used to generate restraints for structure refinement, and not to atom sites in the _atom_site list. The estimated standard deviation of attribute model_Cartn_y in category chem_comp_atom. The x component of the coordinates for this atom in this component specified as orthogonal angstroms. The choice of reference axis frame for the coordinates is arbitrary. The set of coordinates input for the entity here is intended to correspond to the atomic model used to generate restraints for structure refinement, and not to atom sites in the _atom_site list. The estimated standard deviation of attribute model_Cartn_z in category chem_comp_atom. The partial charge assigned to this atom. This data item assigns the atom to a substructure of the component, if appropriate. This data item is a pointer to attribute symbol in category atom_type in the ATOM_TYPE category. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. The value of attribute atom_id in category chem_comp_atom must uniquely identify each atom in each monomer in the CHEM_COMP_ATOM list. The atom identifiers need not be unique over all atoms in the data block; they need only be unique for each atom in a component. Note that this item need not be a number; it can be any unique identifier. Data items in the CHEM_COMP_BOND category record details about the bonds between atoms in a chemical component. Target values may be specified as bond orders, as a distance between the two atoms, or both. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:chem_comp_bondCategory> <PDBx:chem_comp_bond comp_id="phe" atom_id_1="N" atom_id_2="CA"> <PDBx:value_order>sing</PDBx:value_order> <PDBx:value_dist>x.xx</PDBx:value_dist> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond comp_id="phe" atom_id_1="CA" atom_id_2="C"> <PDBx:value_order>sing</PDBx:value_order> <PDBx:value_dist>x.xx</PDBx:value_dist> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond comp_id="phe" atom_id_1="C" atom_id_2="O"> <PDBx:value_order>doub</PDBx:value_order> <PDBx:value_dist>x.xx</PDBx:value_dist> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond comp_id="phe" atom_id_1="CB" atom_id_2="CA"> <PDBx:value_order>sing</PDBx:value_order> <PDBx:value_dist>x.xx</PDBx:value_dist> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond comp_id="phe" atom_id_1="CB" atom_id_2="CG"> <PDBx:value_order>sing</PDBx:value_order> <PDBx:value_dist>x.xx</PDBx:value_dist> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond comp_id="phe" atom_id_1="CG" atom_id_2="CD1"> <PDBx:value_order>arom</PDBx:value_order> <PDBx:value_dist>x.xx</PDBx:value_dist> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond comp_id="phe" atom_id_1="CD1" atom_id_2="CE1"> <PDBx:value_order>arom</PDBx:value_order> <PDBx:value_dist>x.xx</PDBx:value_dist> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond comp_id="phe" atom_id_1="CE1" atom_id_2="CZ"> <PDBx:value_order>arom</PDBx:value_order> <PDBx:value_dist>x.xx</PDBx:value_dist> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond comp_id="phe" atom_id_1="CZ" atom_id_2="CE2"> <PDBx:value_order>arom</PDBx:value_order> <PDBx:value_dist>x.xx</PDBx:value_dist> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond comp_id="phe" atom_id_1="CE2" atom_id_2="CD2"> <PDBx:value_order>arom</PDBx:value_order> <PDBx:value_dist>x.xx</PDBx:value_dist> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond comp_id="phe" atom_id_1="CD2" atom_id_2="CG"> <PDBx:value_order>arom</PDBx:value_order> <PDBx:value_dist>x.xx</PDBx:value_dist> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond comp_id="val" atom_id_1="N" atom_id_2="CA"> <PDBx:value_order>sing</PDBx:value_order> <PDBx:value_dist>x.xx</PDBx:value_dist> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond comp_id="val" atom_id_1="CA" atom_id_2="C"> <PDBx:value_order>sing</PDBx:value_order> <PDBx:value_dist>x.xx</PDBx:value_dist> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond comp_id="val" atom_id_1="C" atom_id_2="O"> <PDBx:value_order>doub</PDBx:value_order> <PDBx:value_dist>x.xx</PDBx:value_dist> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond comp_id="val" atom_id_1="CB" atom_id_2="CA"> <PDBx:value_order>sing</PDBx:value_order> <PDBx:value_dist>x.xx</PDBx:value_dist> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond comp_id="val" atom_id_1="CB" atom_id_2="CG1"> <PDBx:value_order>sing</PDBx:value_order> <PDBx:value_dist>x.xx</PDBx:value_dist> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond comp_id="val" atom_id_1="CB" atom_id_2="CG2"> <PDBx:value_order>sing</PDBx:value_order> <PDBx:value_dist>x.xx</PDBx:value_dist> </PDBx:chem_comp_bond> </PDBx:chem_comp_bondCategory> The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a distance. The estimated standard deviation of attribute value_dist in category chem_comp_bond. The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a bond order. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. The id of the first of the two atoms that define the bond. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. The id of the second of the two atoms that define the bond. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. Data items in the CHEM_COMP_CHIR category provide detail about the chiral centers in a chemical component. The atoms bonded to the chiral atom are specified in the CHEM_COMP_CHIR_ATOM category. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:chem_comp_chirCategory> <PDBx:chem_comp_chir comp_id="phe" id="phe1"> <PDBx:atom_id>CA</PDBx:atom_id> </PDBx:chem_comp_chir> <PDBx:chem_comp_chir comp_id="val" id="val1"> <PDBx:atom_id>CA</PDBx:atom_id> </PDBx:chem_comp_chir> </PDBx:chem_comp_chirCategory> The chiral configuration of the atom that is a chiral center. The id of the atom that is a chiral center. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. The total number of atoms bonded to the atom specified by attribute atom_id in category chem_comp_chir. The number of non-hydrogen atoms bonded to the atom specified by attribute atom_id in category chem_comp_chir. A flag to indicate whether a chiral volume should match the standard value in both magnitude and sign, or in magnitude only. The chiral volume, V(c), for chiral centers that involve a chiral atom bonded to three non-hydrogen atoms and one hydrogen atom. V~c~ = V1 * (V2 X V3) V1 = the vector distance from the atom specified by attribute atom_id in category chem_comp_chir to the first atom in the CHEM_COMP_CHIR_ATOM list V2 = the vector distance from the atom specified by attribute atom_id in category chem_comp_chir to the second atom in the CHEM_COMP_CHIR_ATOM list V3 = the vector distance from the atom specified by attribute atom_id in category chem_comp_chir to the third atom in the CHEM_COMP_CHIR_ATOM list * = the vector dot product X = the vector cross product The estimated standard deviation of attribute volume_three in category chem_comp_chir. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. The value of attribute id in category chem_comp_chir must uniquely identify a record in the CHEM_COMP_CHIR list. Data items in the CHEM_COMP_CHIR_ATOM category enumerate the atoms bonded to a chiral atom within a chemical component. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:chem_comp_chir_atomCategory> <PDBx:chem_comp_chir_atom comp_id="phe" chir_id="1" atom_id="N"></PDBx:chem_comp_chir_atom> <PDBx:chem_comp_chir_atom comp_id="phe" chir_id="1" atom_id="C"></PDBx:chem_comp_chir_atom> <PDBx:chem_comp_chir_atom comp_id="phe" chir_id="1" atom_id="CB"></PDBx:chem_comp_chir_atom> <PDBx:chem_comp_chir_atom comp_id="val" chir_id="1" atom_id="N"></PDBx:chem_comp_chir_atom> <PDBx:chem_comp_chir_atom comp_id="val" chir_id="1" atom_id="C"></PDBx:chem_comp_chir_atom> <PDBx:chem_comp_chir_atom comp_id="val" chir_id="1" atom_id="CB"></PDBx:chem_comp_chir_atom> </PDBx:chem_comp_chir_atomCategory> The estimated standard deviation of the position of this atom from the plane defined by all of the atoms in the plane. This data item is a pointer to attribute id in category chem_comp_chir in the CHEM_COMP_CHIR category. The id of an atom bonded to the chiral atom. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. Data items in the CHEM_COMP_LINK category give details about the linkages between chemical components. Example 1 - from nucleotide external reference dictionary Nucleic Database Project 1997. <PDBx:chem_comp_linkCategory> <PDBx:chem_comp_link link_id="ribose_adenine"> <PDBx:type_comp_1>ribose</PDBx:type_comp_1> <PDBx:type_comp_2>adenine</PDBx:type_comp_2> <PDBx:details> Defines the linkage between adenine base and ribose sugar</PDBx:details> </PDBx:chem_comp_link> </PDBx:chem_comp_linkCategory> A description of special aspects of a linkage between chemical components in the structure. The type of the first of the two components joined by the linkage. This data item is a pointer to attribute type in category chem_comp in the CHEM_COMP category. The type of the second of the two components joined by the linkage. This data item is a pointer to attribute type in category chem_comp in the CHEM_COMP category. This data item is a pointer to attribute id in category chem_link in the CHEM_LINK category. Data items in the CHEM_COMP_PLANE category provide identifiers for the planes in a chemical component. The atoms in the plane are specified in the CHEM_COMP_PLANE_ATOM category. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:chem_comp_planeCategory> <PDBx:chem_comp_plane comp_id="phe" id="phe1"></PDBx:chem_comp_plane> </PDBx:chem_comp_planeCategory> The total number of atoms in the plane. The number of non-hydrogen atoms in the plane. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. The value of attribute id in category chem_comp_plane must uniquely identify a record in the CHEM_COMP_PLANE list. Data items in the CHEM_COMP_PLANE_ATOM category enumerate the atoms in a plane within a chemical component. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:chem_comp_plane_atomCategory> <PDBx:chem_comp_plane_atom plane_id="phe1" comp_id="phe" atom_id="CB"></PDBx:chem_comp_plane_atom> <PDBx:chem_comp_plane_atom plane_id="phe1" comp_id="phe" atom_id="CG"></PDBx:chem_comp_plane_atom> <PDBx:chem_comp_plane_atom plane_id="phe1" comp_id="phe" atom_id="CD1"></PDBx:chem_comp_plane_atom> <PDBx:chem_comp_plane_atom plane_id="phe1" comp_id="phe" atom_id="CE1"></PDBx:chem_comp_plane_atom> <PDBx:chem_comp_plane_atom plane_id="phe1" comp_id="phe" atom_id="CZ"></PDBx:chem_comp_plane_atom> <PDBx:chem_comp_plane_atom plane_id="phe1" comp_id="phe" atom_id="CE2"></PDBx:chem_comp_plane_atom> <PDBx:chem_comp_plane_atom plane_id="phe1" comp_id="phe" atom_id="CD2"></PDBx:chem_comp_plane_atom> </PDBx:chem_comp_plane_atomCategory> This data item is the standard deviation of the out-of-plane distance for this atom. This data item is a pointer to attribute id in category chem_comp_plane in the CHEM_COMP_PLANE category. The id of an atom involved in the plane. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. Data items in the CHEM_COMP_TOR category record details about the torsion angles in a chemical component. As torsion angles can have more than one target value, the target values are specified in the CHEM_COMP_TOR_VALUE category. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:chem_comp_torCategory> <PDBx:chem_comp_tor comp_id="phe" id="phe_chi1"> <PDBx:atom_id_1>N</PDBx:atom_id_1> <PDBx:atom_id_2>CA</PDBx:atom_id_2> <PDBx:atom_id_3>CB</PDBx:atom_id_3> <PDBx:atom_id_4>CG</PDBx:atom_id_4> </PDBx:chem_comp_tor> <PDBx:chem_comp_tor comp_id="phe" id="phe_chi2"> <PDBx:atom_id_1>CA</PDBx:atom_id_1> <PDBx:atom_id_2>CB</PDBx:atom_id_2> <PDBx:atom_id_3>CG</PDBx:atom_id_3> <PDBx:atom_id_4>CD1</PDBx:atom_id_4> </PDBx:chem_comp_tor> <PDBx:chem_comp_tor comp_id="phe" id="phe_ring1"> <PDBx:atom_id_1>CB</PDBx:atom_id_1> <PDBx:atom_id_2>CG</PDBx:atom_id_2> <PDBx:atom_id_3>CD1</PDBx:atom_id_3> <PDBx:atom_id_4>CE1</PDBx:atom_id_4> </PDBx:chem_comp_tor> <PDBx:chem_comp_tor comp_id="phe" id="phe_ring2"> <PDBx:atom_id_1>CB</PDBx:atom_id_1> <PDBx:atom_id_2>CG</PDBx:atom_id_2> <PDBx:atom_id_3>CD2</PDBx:atom_id_3> <PDBx:atom_id_4>CE2</PDBx:atom_id_4> </PDBx:chem_comp_tor> <PDBx:chem_comp_tor comp_id="phe" id="phe_ring3"> <PDBx:atom_id_1>CG</PDBx:atom_id_1> <PDBx:atom_id_2>CD1</PDBx:atom_id_2> <PDBx:atom_id_3>CE1</PDBx:atom_id_3> <PDBx:atom_id_4>CZ</PDBx:atom_id_4> </PDBx:chem_comp_tor> <PDBx:chem_comp_tor comp_id="phe" id="phe_ring4"> <PDBx:atom_id_1>CD1</PDBx:atom_id_1> <PDBx:atom_id_2>CE1</PDBx:atom_id_2> <PDBx:atom_id_3>CZ</PDBx:atom_id_3> <PDBx:atom_id_4>CE2</PDBx:atom_id_4> </PDBx:chem_comp_tor> <PDBx:chem_comp_tor comp_id="phe" id="phe_ring5"> <PDBx:atom_id_1>CE1</PDBx:atom_id_1> <PDBx:atom_id_2>CZ</PDBx:atom_id_2> <PDBx:atom_id_3>CE2</PDBx:atom_id_3> <PDBx:atom_id_4>CD2</PDBx:atom_id_4> </PDBx:chem_comp_tor> </PDBx:chem_comp_torCategory> The id of the first of the four atoms that define the torsion angle. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. The id of the second of the four atoms that define the torsion angle. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. The id of the third of the four atoms that define the torsion angle. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. The id of the fourth of the four atoms that define the torsion angle. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. The value of attribute id in category chem_comp_tor must uniquely identify a record in the CHEM_COMP_TOR list. Data items in the CHEM_COMP_TOR_VALUE category record details about the target values for the torsion angles enumerated in the CHEM_COMP_TOR list. Target values may be specified as angles in degrees, as a distance between the first and fourth atoms, or both. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:chem_comp_tor_valueCategory> <PDBx:chem_comp_tor_value tor_id="phe_chi1" comp_id="phe"> <PDBx:angle>-60.0</PDBx:angle> <PDBx:dist>2.88</PDBx:dist> </PDBx:chem_comp_tor_value> <PDBx:chem_comp_tor_value tor_id="phe_chi1" comp_id="phe"> <PDBx:angle>180.0</PDBx:angle> <PDBx:dist>3.72</PDBx:dist> </PDBx:chem_comp_tor_value> <PDBx:chem_comp_tor_value tor_id="phe_chi1" comp_id="phe"> <PDBx:angle>60.0</PDBx:angle> <PDBx:dist>2.88</PDBx:dist> </PDBx:chem_comp_tor_value> <PDBx:chem_comp_tor_value tor_id="phe_chi2" comp_id="phe"> <PDBx:angle>90.0</PDBx:angle> <PDBx:dist>3.34</PDBx:dist> </PDBx:chem_comp_tor_value> <PDBx:chem_comp_tor_value tor_id="phe_chi2" comp_id="phe"> <PDBx:angle>-90.0</PDBx:angle> <PDBx:dist>3.34</PDBx:dist> </PDBx:chem_comp_tor_value> <PDBx:chem_comp_tor_value tor_id="phe_ring1" comp_id="phe"> <PDBx:angle>180.0</PDBx:angle> <PDBx:dist>3.75</PDBx:dist> </PDBx:chem_comp_tor_value> <PDBx:chem_comp_tor_value tor_id="phe_ring2" comp_id="phe"> <PDBx:angle>180.0</PDBx:angle> <PDBx:dist>3.75</PDBx:dist> </PDBx:chem_comp_tor_value> <PDBx:chem_comp_tor_value tor_id="phe_ring3" comp_id="phe"> <PDBx:angle>0.0</PDBx:angle> <PDBx:dist>2.80</PDBx:dist> </PDBx:chem_comp_tor_value> <PDBx:chem_comp_tor_value tor_id="phe_ring4" comp_id="phe"> <PDBx:angle>0.0</PDBx:angle> <PDBx:dist>2.80</PDBx:dist> </PDBx:chem_comp_tor_value> <PDBx:chem_comp_tor_value tor_id="phe_ring5" comp_id="phe"> <PDBx:angle>0.0</PDBx:angle> <PDBx:dist>2.80</PDBx:dist> </PDBx:chem_comp_tor_value> </PDBx:chem_comp_tor_valueCategory> A value that should be taken as a potential target value for the torsion angle associated with the specified atoms, expressed in degrees. The estimated standard deviation of attribute angle in category chem_comp_tor_value. A value that should be taken as a potential target value for the torsion angle associated with the specified atoms, expressed as the distance between the atoms specified by _chem_comp_tor.atom_id_1 and _chem_comp_tor.atom_id_4 in the referenced record in the CHEM_COMP_TOR list. Note that the torsion angle cannot be fully specified by a distance (for instance, a torsion angle of -60 will yield the same distance as a 60 degree angle). However the distance specification can be useful for refinement in situations in which the angle is already close to the desired value. The estimated standard deviation of attribute dist_esd in category chem_comp_tor_value. This data item is a pointer to attribute id in category chem_comp_tor in the CHEM_COMP_TOR category. This data item is a pointer to attribute comp_id in category chem_comp_atom in the CHEM_COMP_ATOM category. Data items in the CHEM_LINK category give details about the linkages between chemical groups. A description of special aspects of a linkage between chemical components in the structure. The value of attribute id in category chem_link must uniquely identify each item in the CHEM_LINK list. peptide oligosaccharide 1,4 DNA Data items in the CHEM_LINK_ANGLE category record details about angles in a linkage between chemical groups. Example 1 - Engh and Huber parameters as interpreted by J. P. Priestle <PDBx:chem_link_angleCategory> <PDBx:chem_link_angle link_id="PEPTIDE" atom_id_1="N" atom_id_2="CA" atom_id_3="C"> <PDBx:value_angle>111.2</PDBx:value_angle> <PDBx:value_angle_esd>2.8</PDBx:value_angle_esd> <PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id> <PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id> <PDBx:atom_3_comp_id>1</PDBx:atom_3_comp_id> </PDBx:chem_link_angle> <PDBx:chem_link_angle link_id="PEPTIDE" atom_id_1="CA" atom_id_2="C" atom_id_3="O"> <PDBx:value_angle>120.8</PDBx:value_angle> <PDBx:value_angle_esd>1.7</PDBx:value_angle_esd> <PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id> <PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id> <PDBx:atom_3_comp_id>1</PDBx:atom_3_comp_id> </PDBx:chem_link_angle> <PDBx:chem_link_angle link_id="PEPTIDE" atom_id_1="CA" atom_id_2="C" atom_id_3="N"> <PDBx:value_angle>116.2</PDBx:value_angle> <PDBx:value_angle_esd>2.0</PDBx:value_angle_esd> <PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id> <PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id> <PDBx:atom_3_comp_id>2</PDBx:atom_3_comp_id> </PDBx:chem_link_angle> <PDBx:chem_link_angle link_id="PEPTIDE" atom_id_1="O" atom_id_2="C" atom_id_3="N"> <PDBx:value_angle>123.0</PDBx:value_angle> <PDBx:value_angle_esd>1.6</PDBx:value_angle_esd> <PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id> <PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id> <PDBx:atom_3_comp_id>2</PDBx:atom_3_comp_id> </PDBx:chem_link_angle> <PDBx:chem_link_angle link_id="PEPTIDE" atom_id_1="C" atom_id_2="N" atom_id_3="CA"> <PDBx:value_angle>121.7</PDBx:value_angle> <PDBx:value_angle_esd>1.8</PDBx:value_angle_esd> <PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id> <PDBx:atom_2_comp_id>2</PDBx:atom_2_comp_id> <PDBx:atom_3_comp_id>2</PDBx:atom_3_comp_id> </PDBx:chem_link_angle> </PDBx:chem_link_angleCategory> This data item indicates whether atom 1 is found in the first or the second of the two components connected by the linkage. This data item indicates whether atom 2 is found in the first or the second of the two components connected by the linkage. This data item indicates whether atom 3 is found in the first or the second of the two components connected by the linkage. The value that should be taken as the target value for the angle associated with the specified atoms, expressed in degrees. The estimated standard deviation of attribute value_angle in category chem_link_angle. The value that should be taken as the target value for the angle associated with the specified atoms, expressed as the distance between the atoms specified by attribute atom_id_1 in category chem_comp_angle and attribute atom_id_3 in category chem_comp_angle. The estimated standard deviation of attribute value_dist_esd in category chem_comp_angle. This data item is a pointer to attribute id in category chem_link in the CHEM_LINK category. The id of the first of the three atoms that define the angle. An atom with this id must exist in the component of the type specified by _chem_comp_link.type_1 (or _chem_comp_link.type_2, where the appropriate data item is indated by the value of attribute atom_1_comp_id) in category chem_comp_link. The id of the second of the three atoms that define the angle. The second atom is taken to be the apex of the angle. An atom with this id must exist in the component of the type specified by _chem_comp_link.type_1 (or _chem_comp_link.type_2, where the appropriate data item is indated by the value of attribute atom_2_comp_id) in category chem_comp_link. The id of the third of the three atoms that define the angle. An atom with this id must exist in the component of the type specified by _chem_comp_link.type_1 (or _chem_comp_link.type_2, where the appropriate data item is indated by the value of attribute atom_3_comp_id) in category chem_comp_link. Data items in the CHEM_LINK_BOND category record details about bonds in a linkage between components in the chemical structure. Example 1 - Engh and Huber parameters as interpreted by J. P. Priestle <PDBx:chem_link_bondCategory> <PDBx:chem_link_bond link_id="PEPTIDE" atom_id_1="N" atom_id_2="CA"> <PDBx:value_dist>1.458</PDBx:value_dist> <PDBx:value_dist_esd>0.019</PDBx:value_dist_esd> <PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id> <PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id> </PDBx:chem_link_bond> <PDBx:chem_link_bond link_id="PEPTIDE" atom_id_1="CA" atom_id_2="C"> <PDBx:value_dist>1.525</PDBx:value_dist> <PDBx:value_dist_esd>0.021</PDBx:value_dist_esd> <PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id> <PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id> </PDBx:chem_link_bond> <PDBx:chem_link_bond link_id="PEPTIDE" atom_id_1="C" atom_id_2="N"> <PDBx:value_dist>1.329</PDBx:value_dist> <PDBx:value_dist_esd>0.014</PDBx:value_dist_esd> <PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id> <PDBx:atom_2_comp_id>2</PDBx:atom_2_comp_id> </PDBx:chem_link_bond> <PDBx:chem_link_bond link_id="PEPTIDE" atom_id_1="C" atom_id_2="O"> <PDBx:value_dist>1.231</PDBx:value_dist> <PDBx:value_dist_esd>0.020</PDBx:value_dist_esd> <PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id> <PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id> </PDBx:chem_link_bond> </PDBx:chem_link_bondCategory> This data item indicates whether atom 1 is found in the first or the second of the two components connected by the linkage. This data item indicates whether atom 2 is found in the first or the second of the two chemical components connected by the linkage. The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a distance. The estimated standard deviation of attribute value_dist_esd in category chem_link_bond. The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a bond order. This data item is a pointer to attribute id in category chem_link in the CHEM_LINK category. The id of the first of the two atoms that define the bond. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. The id of the second of the two atoms that define the bond. As this data item does not point to a specific atom in a specific component, it is not a child in the linkage sense. Data items in the CHEM_LINK_CHIR category provide detail about the chiral centers in a linkage between two chemical components. The atoms bonded to the chiral atom are specified in the CHEM_LINK_CHIR_ATOM category. Example 1 - based on This data item indicates whether the chiral atom is found in the first or the second of the two component connected by the linkage. The chiral configuration of the atom that is a chiral center. The id of the atom that is a chiral center. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. The total number of atoms bonded to the atom specified by attribute atom_id in category chem_link_chir. The number of non-hydrogen atoms bonded to the atom specified by attribute atom_id in category chem_link_chir. A flag to indicate whether a chiral volume should match the standard value in both magnitude and sign, or in magnitude only. The chiral volume, V(c), for chiral centers that involve a chiral atom bonded to three non-hydrogen atoms and one hydrogen atom. V~c~ = V1 * (V2 X V3) V1 = the vector distance from the atom specified by attribute atom_id in category chem_link_chir to the first atom in the CHEM_LINK_CHIR_ATOM list V2 = the vector distance from the atom specified by attribute atom_id in category chem_link_chir to the second atom in the CHEM_LINK_CHIR_ATOM list V3 = the vector distance from the atom specified by attribute atom_id in category chem_link_chir to the third atom in the CHEM_LINK_CHIR_ATOM list * = the vector dot product X = the vector cross product The estimated standard deviation of attribute volume_three in category chem_link_chir. This data item is a pointer to attribute id in category chem_link in the CHEM_LINK category. The value of attribute id in category chem_link_chir must uniquely identify a record in the CHEM_LINK_CHIR list. Data items in the CHEM_LINK_CHIR_ATOM category enumerate the atoms bonded to a chiral atom in a linkage between two chemical components. Example 1 - based on This data item indicates whether the atom bonded to a chiral atom is found in the first or the second of the two components connected by the linkage. The estimated standard deviation of the position of this atom from the plane defined by all of the atoms in the plane. This data item is a pointer to attribute id in category chem_link_chir in the CHEM_LINK_CHIR category. The id of an atom bonded to the chiral atom. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. Data items in the CHEM_LINK_PLANE category provide identifiers for the planes in a linkage between two chemical components. The atoms in the plane are specified in the CHEM_LINK_PLANE_ATOM category. Example 1 - based on The total number of atoms in the plane. The number of non-hydrogen atoms in the plane. This data item is a pointer to attribute id in category chem_link in the CHEM_LINK category. The value of attribute id in category chem_link_plane must uniquely identify a record in the CHEM_LINK_PLANE list. Data items in the CHEM_LINK_PLANE_ATOM category enumerate the atoms in a plane in a linkage between two chemical components. Example 1 - based on This data item indicates whether the atom in a plane is found in the first or the second of the two components connected by the linkage. This data item is a pointer to attribute id in category chem_link_plane in the CHEM_LINK_PLANE category. The id of an atom involved in the plane. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. Data items in the CHEM_LINK_TOR category record details about the torsion angles in a linkage between two chemical components. As torsion angles can have more than one target value, the target values are specified in the CHEM_LINK_TOR_VALUE category. Example 1 - based on This data item indicates whether atom 1 is found in the first or the second of the two components connected by the linkage. This data item indicates whether atom 2 is found in the first or the second of the two components connected by the linkage. This data item indicates whether atom 3 is found in the first or the second of the two components connected by the linkage. This data item indicates whether atom 4 is found in the first or the second of the two components connected by the linkage. The id of the first of the four atoms that define the torsion angle. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. The id of the second of the four atoms that define the torsion angle. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. The id of the third of the four atoms that define the torsion angle. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. The id of the fourth of the four atoms that define the torsion angle. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. This data item is a pointer to attribute id in category chem_link in the CHEM_LINK category. The value of attribute id in category chem_link_tor must uniquely identify a record in the CHEM_LINK_TOR list. Data items in the CHEM_LINK_TOR_VALUE category record details about the target values for the torsion angles enumerated in the CHEM_LINK_TOR list. Target values may be specified as angles in degrees, as a distance between the first and fourth atoms, or both. Example 1 - based on A value that should be taken as a potential target value for the torsion angle associated with the specified atoms, expressed in degrees. The estimated standard deviation of attribute angle in category chem_link_tor_value. A value that should be taken as a potential target value for the torsion angle associated with the specified atoms, expressed as the distance between the atoms specified by _chem_link_tor.atom_id_1 and _chem_link_tor.atom_id_4 in the referenced record in the CHEM_LINK_TOR list. Note that the torsion angle cannot be fully specified by a distance (for instance, a torsion angle of -60 will yield the same distance as a 60 degree angle). However the distance specification can be useful for refinement in situations in which the angle is already close to the desired value. The estimated standard deviation of attribute dist_esd in category chem_link_tor_value. This data item is a pointer to attribute id in category chem_link_tor in the CHEM_LINK_TOR category. Data items in the CHEMICAL category would not in general be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL category record details about the composition and chemical properties of the compounds. The formula data items must agree with those that specify the density, unit-cell and Z values. Example 1 - based on data set 9597gaus of Alyea, Ferguson & Kannan [(1996). Acta Cryst. C52, 765-767]. <PDBx:chemicalCategory> <PDBx:chemical entry_id="9597gaus"> <PDBx:name_systematic>trans-bis(tricyclohexylphosphine)tetracarbonylmolybdenum(0)</PDBx:name_systematic> </PDBx:chemical> </PDBx:chemicalCategory> Description of the source of the compound under study, or of the parent molecule if a simple derivative is studied. This includes the place of discovery for minerals or the actual source of a natural product. From Norilsk (USSR) Extracted from the bark of Cinchona Naturalis The temperature in kelvins at which a crystalline solid changes to a liquid. Trivial name by which the compound is commonly known. 1-bromoestradiol Mineral name accepted by the International Mineralogical Association. Use only for natural minerals. See also attribute compound_source in category chemical. chalcopyrite Commonly used structure-type name. Usually only applied to minerals or inorganic compounds. perovskite sphalerite A15 IUPAC or Chemical Abstracts full name of compound. 1-bromoestra-1,3,5(10)-triene-3,17\b-diol This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the CHEMICAL_CONN_ATOM category would not, in general, be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND categories record details about the 2D chemical structure of the molecular species. They allow a 2D chemical diagram to be reconstructed for use in a publication or in a database search for structural and substructural relationships. The CHEMICAL_CONN_ATOM data items provide information about the chemical properties of the atoms in the structure. In cases where crystallographic and molecular symmetry elements coincide they must also contain symmetry-generated atoms, so that the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND data items will always describe a complete chemical entity. Example 1 - based on data set DPTD of Yamin, Suwandi, Fun, Sivakumar & bin Shawkataly [(1996). Acta Cryst. C52, 951-953]. <PDBx:chemical_conn_atomCategory> <PDBx:chemical_conn_atom number="1"> <PDBx:type_symbol>S</PDBx:type_symbol> <PDBx:display_x>.39</PDBx:display_x> <PDBx:display_y>.81</PDBx:display_y> <PDBx:NCA>1</PDBx:NCA> <PDBx:NH>0</PDBx:NH> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="2"> <PDBx:type_symbol>S</PDBx:type_symbol> <PDBx:display_x>.39</PDBx:display_x> <PDBx:display_y>.96</PDBx:display_y> <PDBx:NCA>2</PDBx:NCA> <PDBx:NH>0</PDBx:NH> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="3"> <PDBx:type_symbol>N</PDBx:type_symbol> <PDBx:display_x>.14</PDBx:display_x> <PDBx:display_y>.88</PDBx:display_y> <PDBx:NCA>3</PDBx:NCA> <PDBx:NH>0</PDBx:NH> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="4"> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:display_x>.33</PDBx:display_x> <PDBx:display_y>.88</PDBx:display_y> <PDBx:NCA>3</PDBx:NCA> <PDBx:NH>0</PDBx:NH> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="5"> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:display_x>.11</PDBx:display_x> <PDBx:display_y>.96</PDBx:display_y> <PDBx:NCA>2</PDBx:NCA> <PDBx:NH>2</PDBx:NH> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="6"> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:display_x>.03</PDBx:display_x> <PDBx:display_y>.96</PDBx:display_y> <PDBx:NCA>2</PDBx:NCA> <PDBx:NH>2</PDBx:NH> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="7"> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:display_x>.03</PDBx:display_x> <PDBx:display_y>.80</PDBx:display_y> <PDBx:NCA>2</PDBx:NCA> <PDBx:NH>2</PDBx:NH> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="8"> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:display_x>.11</PDBx:display_x> <PDBx:display_y>.80</PDBx:display_y> <PDBx:NCA>2</PDBx:NCA> <PDBx:NH>2</PDBx:NH> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="9"> <PDBx:type_symbol>S</PDBx:type_symbol> <PDBx:display_x>.54</PDBx:display_x> <PDBx:display_y>.81</PDBx:display_y> <PDBx:NCA>1</PDBx:NCA> <PDBx:NH>0</PDBx:NH> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="10"> <PDBx:type_symbol>S</PDBx:type_symbol> <PDBx:display_x>.54</PDBx:display_x> <PDBx:display_y>.96</PDBx:display_y> <PDBx:NCA>2</PDBx:NCA> <PDBx:NH>0</PDBx:NH> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="11"> <PDBx:type_symbol>N</PDBx:type_symbol> <PDBx:display_x>.80</PDBx:display_x> <PDBx:display_y>.88</PDBx:display_y> <PDBx:NCA>3</PDBx:NCA> <PDBx:NH>0</PDBx:NH> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="12"> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:display_x>.60</PDBx:display_x> <PDBx:display_y>.88</PDBx:display_y> <PDBx:NCA>3</PDBx:NCA> <PDBx:NH>0</PDBx:NH> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="13"> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:display_x>.84</PDBx:display_x> <PDBx:display_y>.96</PDBx:display_y> <PDBx:NCA>2</PDBx:NCA> <PDBx:NH>2</PDBx:NH> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="14"> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:display_x>.91</PDBx:display_x> <PDBx:display_y>.96</PDBx:display_y> <PDBx:NCA>2</PDBx:NCA> <PDBx:NH>2</PDBx:NH> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="15"> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:display_x>.91</PDBx:display_x> <PDBx:display_y>.80</PDBx:display_y> <PDBx:NCA>2</PDBx:NCA> <PDBx:NH>2</PDBx:NH> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="16"> <PDBx:type_symbol>C</PDBx:type_symbol> <PDBx:display_x>.84</PDBx:display_x> <PDBx:display_y>.80</PDBx:display_y> <PDBx:NCA>2</PDBx:NCA> <PDBx:NH>2</PDBx:NH> </PDBx:chemical_conn_atom> </PDBx:chemical_conn_atomCategory> The number of connected atoms excluding terminal hydrogen atoms. The total number of hydrogen atoms attached to this atom, regardless of whether they are included in the refinement or the ATOM_SITE list. This number is the same as attribute attached_hydrogens in category atom_site only if none of the hydrogen atoms appear in the ATOM_SITE list. The net integer charge assigned to this atom. This is the formal charge assignment normally found in chemical diagrams. for an ammonium nitrogen 1 for a chloride ion -1 The 2D Cartesian x coordinate of the position of this atom in a recognisable chemical diagram. The coordinate origin is at the lower left corner, the x axis is horizontal and the y axis is vertical. The coordinates must lie in the range 0.0 to 1.0. These coordinates can be obtained from projections of a suitable uncluttered view of the molecular structure. If absent, values will be assigned by the journal or database staff. The 2D Cartesian y coordinate of the position of this atom in a recognisable chemical diagram. The coordinate origin is at the lower left corner, the x axis is horizontal and the y axis is vertical. The coordinates must lie in the range 0.0 to 1.0. These coordinates can be obtained from projections of a suitable uncluttered view of the molecular structure. If absent, values will be assigned by the journal or database staff. This data item is a pointer to attribute symbol in category atom_type in the ATOM_TYPE category. The chemical sequence number to be associated with this atom. Within an ATOM_SITE list this number must match with one of the attribute chemical_conn_number in category atom_site values. Data items in the CHEMICAL_CONN_BOND category would not, in general, be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND categories record details about the 2D chemical structure of the molecular species. They allow a 2D chemical diagram to be reconstructed for use in a publication or in a database search for structural and substructural relationships. The CHEMICAL_CONN_BOND data items specify the connections between the atoms in the CHEMICAL_CONN_ATOM list and the nature of the chemical bond between these atoms. Example 1 - based on data set DPTD of Yamin, Suwandi, Fun, Sivakumar & bin Shawkataly [(1996). Acta Cryst. C52, 951-953]. <PDBx:chemical_conn_bondCategory> <PDBx:chemical_conn_bond atom_1="4" atom_2="1"> <PDBx:type>doub</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="4" atom_2="3"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="4" atom_2="2"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="5" atom_2="3"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="6" atom_2="5"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="7" atom_2="6"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="8" atom_2="7"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="8" atom_2="3"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="10" atom_2="2"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="12" atom_2="9"> <PDBx:type>doub</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="12" atom_2="11"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="12" atom_2="10"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="13" atom_2="11"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="14" atom_2="13"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="15" atom_2="14"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="16" atom_2="15"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="16" atom_2="11"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="17" atom_2="5"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="18" atom_2="5"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="19" atom_2="6"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="20" atom_2="6"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="21" atom_2="7"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="22" atom_2="7"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="23" atom_2="8"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="24" atom_2="8"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="25" atom_2="13"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="26" atom_2="13"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="27" atom_2="14"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="28" atom_2="14"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="29" atom_2="15"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="30" atom_2="15"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="31" atom_2="16"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="32" atom_2="16"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> </PDBx:chemical_conn_bondCategory> The chemical bond type associated with the connection between the two sites attribute atom_1 in category chemical_conn_bond and attribute atom_2 in category chemical_conn_bond. This data item is a pointer to attribute number in category chemical_conn_atom in the CHEMICAL_CONN_ATOM category. This data item is a pointer to attribute number in category chemical_conn_atom in the CHEMICAL_CONN_ATOM category. Data items in the CHEMICAL_FORMULA category would not, in general, be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL_FORMULA category specify the composition and chemical properties of the compound. The formula data items must agree with those that specify the density, unit cell and Z values. The following rules apply to the construction of the data items _chemical_formula.analytical, _chemical_formula.structural and attribute sum in category chemical_formula. For the data item attribute moiety in category chemical_formula the formula construction is broken up into residues or moieties, i.e. groups of atoms that form a molecular unit or molecular ion. The rules given below apply within each moiety but different requirements apply to the way that moieties are connected (see attribute moiety). in category chemical_formula 1. Only recognised element symbols may be used. 2. Each element symbol is followed by a 'count' number. A count of '1' may be omitted. 3. A space or parenthesis must separate each cluster of (element symbol + count). 4. Where a group of elements is enclosed in parentheses, the multiplier for the group must follow the closing parentheses. That is, all element and group multipliers are assumed to be printed as subscripted numbers. [An exception to this rule exists for attribute moiety in category chemical_formula formulae where pre- and post-multipliers are permitted for molecular units]. 5. Unless the elements are ordered in a manner that corresponds to their chemical structure, as in attribute structural in category chemical_formula the order of the elements within any group or moiety should be: C, H followed by the other elements in alphabetical order of their symbol. This is the 'Hill' system used by Chemical Abstracts. This ordering is used in _chemical_formula.moiety and _chemical_formula.sum. Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. <PDBx:chemical_formulaCategory> <PDBx:chemical_formula entry_id="TOZ"> <PDBx:moiety>C18 H25 N O3</PDBx:moiety> <PDBx:sum>C18 H25 N O3</PDBx:sum> <PDBx:weight>303.40</PDBx:weight> </PDBx:chemical_formula> </PDBx:chemical_formulaCategory> Formula determined by standard chemical analysis including trace elements. See the CHEMICAL_FORMULA category description for rules for writing chemical formulae. Parentheses are used only for standard uncertainties (e.s.d.'s). Fe2.45(2) Ni1.60(3) S4 Formula expressed in conformance with IUPAC rules for inorganic and metal-organic compounds where these conflict with the rules for any other CHEMICAL_FORMULA entries. Typically used for formatting a formula in accordance with journal rules. This should appear in the data block in addition to the most appropriate of the other CHEMICAL_FORMULA data names. Ref: IUPAC (1990). Nomenclature of Inorganic Chemistry. Oxford: Blackwell Scientific Publications. [Co Re (C12 H22 P)2 (C O)6].0.5C H3 O H Formula with each discrete bonded residue or ion shown as a separate moiety. See the CHEMICAL_FORUMULA category description for rules for writing chemical formulae. In addition to the general formulae requirements, the following rules apply: 1. Moieties are separated by commas ','. 2. The order of elements within a moiety follows general rule 5 in the CHEMICAL_FORMULA category description. 3. Parentheses are not used within moieties but may surround a moiety. Parentheses may not be nested. 4. Charges should be placed at the end of the moiety. The charge '+' or '-' may be preceded by a numerical multiplier and should be separated from the last (element symbol + count) by a space. Pre- or post-multipliers may be used for individual moieties. C7 H4 Cl Hg N O3 S C12 H17 N4 O S 1+, C6 H2 N3 O7 1- C12 H16 N2 O6, 5(H2 O1) (Cd 2+)3, (C6 N6 Cr 3-)2, 2(H2 O) See the CHEMICAL_FORMULA category description for the rules for writing chemical formulae for inorganics, organometallics, metal complexes etc., in which bonded groups are preserved as discrete entities within parentheses, with post-multipliers as required. The order of the elements should give as much information as possible about the chemical structure. Parentheses may be used and nested as required. This formula should correspond to the structure as actually reported, i.e. trace elements not included in atom type and atom site data should not be included in this formula (see also attribute analytical) in category chemical_formula. Ca ((Cl O3)2 O)2 (H2 O)6 (Pt (N H3)2 (C5 H7 N3 O)2) (Cl O4)2 See the CHEMICAL_FORMULA category description for the rules for writing chemical formulae in which all discrete bonded residues and ions are summed over the constituent elements, following the ordering given in general rule 5 in the CHEMICAL_FORMULA category description. Parentheses are not normally used. C18 H19 N7 O8 S Formula mass in daltons. This mass should correspond to the formulae given under attribute structural in category chemical_formula chemical_formula.moiety or attribute sum in category chemical_formula and, together with the Z value and cell parameters, should yield the density given as attribute density_diffrn in category exptl_crystal. Formula mass in daltons measured by a non-diffraction experiment. This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the CITATION category record details about the literature cited relevant to the contents of the data block. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:citationCategory> <PDBx:citation id="primary"> <PDBx:coordinate_linkage>yes</PDBx:coordinate_linkage> <PDBx:title> Crystallographic analysis of a complex between human immunodeficiency virus type 1 protease and acetyl-pepstatin at 2.0-Angstroms resolution.</PDBx:title> <PDBx:country>US</PDBx:country> <PDBx:journal_abbrev>J. Biol. Chem.</PDBx:journal_abbrev> <PDBx:journal_volume>265</PDBx:journal_volume> <PDBx:page_first>14209</PDBx:page_first> <PDBx:page_last>14219</PDBx:page_last> <PDBx:year>1990</PDBx:year> <PDBx:journal_id_ASTM>HBCHA3</PDBx:journal_id_ASTM> <PDBx:journal_id_ISSN>0021-9258</PDBx:journal_id_ISSN> <PDBx:journal_id_CSD>071</PDBx:journal_id_CSD> <PDBx:details> The publication that directly relates to this coordinate set.</PDBx:details> </PDBx:citation> <PDBx:citation id="2"> <PDBx:coordinate_linkage>no</PDBx:coordinate_linkage> <PDBx:title> Three-dimensional structure of aspartyl-protease from human immunodeficiency virus HIV-1.</PDBx:title> <PDBx:country>UK</PDBx:country> <PDBx:journal_abbrev>Nature</PDBx:journal_abbrev> <PDBx:journal_volume>337</PDBx:journal_volume> <PDBx:page_first>615</PDBx:page_first> <PDBx:page_last>619</PDBx:page_last> <PDBx:year>1989</PDBx:year> <PDBx:journal_id_ASTM>NATUAS</PDBx:journal_id_ASTM> <PDBx:journal_id_ISSN>0028-0836</PDBx:journal_id_ISSN> <PDBx:journal_id_CSD>006</PDBx:journal_id_CSD> <PDBx:details> Determination of the structure of the unliganded enzyme.</PDBx:details> </PDBx:citation> <PDBx:citation id="3"> <PDBx:coordinate_linkage>no</PDBx:coordinate_linkage> <PDBx:title> Crystallization of the aspartylprotease from human immunodeficiency virus, HIV-1.</PDBx:title> <PDBx:country>US</PDBx:country> <PDBx:journal_abbrev>J. Biol. Chem.</PDBx:journal_abbrev> <PDBx:journal_volume>264</PDBx:journal_volume> <PDBx:page_first>1919</PDBx:page_first> <PDBx:page_last>1921</PDBx:page_last> <PDBx:year>1989</PDBx:year> <PDBx:journal_id_ASTM>HBCHA3</PDBx:journal_id_ASTM> <PDBx:journal_id_ISSN>0021-9258</PDBx:journal_id_ISSN> <PDBx:journal_id_CSD>071</PDBx:journal_id_CSD> <PDBx:details> Crystallization of the unliganded enzyme.</PDBx:details> </PDBx:citation> <PDBx:citation id="4"> <PDBx:coordinate_linkage>no</PDBx:coordinate_linkage> <PDBx:title> Human immunodeficiency virus protease. Bacterial expression and characterization of the purified aspartic protease.</PDBx:title> <PDBx:country>US</PDBx:country> <PDBx:journal_abbrev>J. Biol. Chem.</PDBx:journal_abbrev> <PDBx:journal_volume>264</PDBx:journal_volume> <PDBx:page_first>2307</PDBx:page_first> <PDBx:page_last>2312</PDBx:page_last> <PDBx:year>1989</PDBx:year> <PDBx:journal_id_ASTM>HBCHA3</PDBx:journal_id_ASTM> <PDBx:journal_id_ISSN>0021-9258</PDBx:journal_id_ISSN> <PDBx:journal_id_CSD>071</PDBx:journal_id_CSD> <PDBx:details> Expression and purification of the enzyme.</PDBx:details> </PDBx:citation> </PDBx:citationCategory> Abstract for the citation. This is used most when the citation is extracted from a bibliographic database that contains full text or abstract information. The Chemical Abstracts Service (CAS) abstract identifier; relevant for journal articles. The International Standard Book Number (ISBN) code assigned to the book cited; relevant for book chapters. The name of the publisher of the citation; relevant for book chapters. John Wiley and Sons The location of the publisher of the citation; relevant for book chapters. London The title of the book in which the citation appeared; relevant for book chapters. attribute coordinate_linkage in category citation states whether or not this citation is concerned with precisely the set of coordinates given in the data block. If, for instance, the publication described the same structure, but the coordinates had undergone further refinement prior to creation of the data block, the value of this data item would be 'no'. The country of publication; relevant for both journal articles and book chapters. Ascession number used by Medline to categorize a specific bibliographic entry. 89064067 A description of special aspects that describe the relationship of the contents of the data block to the literature item cited. citation relates to this precise coordinate set citation relates to earlier low-resolution structure citation relates to further refinement of structure reported in citation 2 Abbreviated name of the journal cited as given in the Chemical Abstracts Service Source Index. J. Mol. Biol. Full name of the journal cited; relevant for journal articles. Journal of Molecular Biology The American Society for the Testing of Materials (ASTM) code assigned to the journal cited (also referred to as the CODEN designator of the Chemical Abstracts Service); relevant for journal articles. The Cambridge Structural Database (CSD) code assigned to the journal cited; relevant for journal articles. This is also the system used at the Brookhaven Protein Data Bank (PDB). 070 The International Standard Serial Number (ISSN) code assigned to the journal cited; relevant for journal articles. Issue number of the journal cited; relevant for journal articles. 2 Volume number of the journal cited; relevant for journal articles. 174 Language in which the citation appears. german The first page of the citation; relevant for journal articles and book chapters. The last page of the citation; relevant for journal articles and book chapters. Ascession number used by PubMed to categorize a specific bibliographic entry. 12627512 The title of the citation; relevant for both journal articles and book chapters. Structure of Diferric Duck Ovatransferrin at 2.35 \%A Resolution. The year of the citation; relevant for both journal articles and book chapters. 1984 The value of attribute id in category citation must uniquely identify a record in the CITATION list. The attribute id in category citation 'primary' should be used to indicate the citation that the author(s) consider to be the most pertinent to the contents of the data block. Note that this item need not be a number; it can be any unique identifier. primary 1 2 Data items in the CITATION_AUTHOR category record details about the authors associated with the citations in the CITATION list. Example 1 - based on PDB entry 5HVP and/or laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:citation_authorCategory> <PDBx:citation_author citation_id="primary" name="Fitzgerald, P.M.D."> <PDBx:ordinal>1</PDBx:ordinal> </PDBx:citation_author> <PDBx:citation_author citation_id="primary" name="McKeever, B.M."> <PDBx:ordinal>2</PDBx:ordinal> </PDBx:citation_author> <PDBx:citation_author citation_id="primary" name="Van Middlesworth, J.F."> <PDBx:ordinal>3</PDBx:ordinal> </PDBx:citation_author> <PDBx:citation_author citation_id="primary" name="Springer, J.P."> <PDBx:ordinal>4</PDBx:ordinal> </PDBx:citation_author> <PDBx:citation_author citation_id="primary" name="Heimbach, J.C."> <PDBx:ordinal>5</PDBx:ordinal> </PDBx:citation_author> <PDBx:citation_author citation_id="primary" name="Leu, C.-T."> <PDBx:ordinal>6</PDBx:ordinal> </PDBx:citation_author> <PDBx:citation_author citation_id="primary" name="Herber, W.K."> <PDBx:ordinal>7</PDBx:ordinal> </PDBx:citation_author> <PDBx:citation_author citation_id="primary" name="Dixon, R.A.F."> <PDBx:ordinal>8</PDBx:ordinal> </PDBx:citation_author> <PDBx:citation_author citation_id="primary" name="Darke, P.L."> <PDBx:ordinal>9</PDBx:ordinal> </PDBx:citation_author> <PDBx:citation_author citation_id="2" name="Navia, M.A."> <PDBx:ordinal>1</PDBx:ordinal> </PDBx:citation_author> <PDBx:citation_author citation_id="2" name="Fitzgerald, P.M.D."> <PDBx:ordinal>2</PDBx:ordinal> </PDBx:citation_author> <PDBx:citation_author citation_id="2" name="McKeever, B.M."> <PDBx:ordinal>3</PDBx:ordinal> </PDBx:citation_author> <PDBx:citation_author citation_id="2" name="Leu, C.-T."> <PDBx:ordinal>4</PDBx:ordinal> </PDBx:citation_author> <PDBx:citation_author citation_id="2" name="Heimbach, J.C."> <PDBx:ordinal>5</PDBx:ordinal> </PDBx:citation_author> <PDBx:citation_author citation_id="2" name="Herber, W.K."> <PDBx:ordinal>6</PDBx:ordinal> </PDBx:citation_author> <PDBx:citation_author citation_id="2" name="Sigal, I.S."> <PDBx:ordinal>7</PDBx:ordinal> </PDBx:citation_author> <PDBx:citation_author citation_id="2" name="Darke, P.L."> <PDBx:ordinal>8</PDBx:ordinal> </PDBx:citation_author> <PDBx:citation_author citation_id="2" name="Springer, J.P."> <PDBx:ordinal>9</PDBx:ordinal> </PDBx:citation_author> <PDBx:citation_author citation_id="3" name="McKeever, B.M."> <PDBx:ordinal>1</PDBx:ordinal> </PDBx:citation_author> <PDBx:citation_author citation_id="3" name="Navia, M.A."> <PDBx:ordinal>2</PDBx:ordinal> </PDBx:citation_author> <PDBx:citation_author citation_id="3" name="Fitzgerald, P.M.D."> <PDBx:ordinal>3</PDBx:ordinal> </PDBx:citation_author> <PDBx:citation_author citation_id="3" name="Springer, J.P."> <PDBx:ordinal>4</PDBx:ordinal> </PDBx:citation_author> <PDBx:citation_author citation_id="3" name="Leu, C.-T."> <PDBx:ordinal>5</PDBx:ordinal> </PDBx:citation_author> <PDBx:citation_author citation_id="3" name="Heimbach, J.C."> <PDBx:ordinal>6</PDBx:ordinal> </PDBx:citation_author> <PDBx:citation_author citation_id="3" name="Herber, W.K."> <PDBx:ordinal>7</PDBx:ordinal> </PDBx:citation_author> <PDBx:citation_author citation_id="3" name="Sigal, I.S."> <PDBx:ordinal>8</PDBx:ordinal> </PDBx:citation_author> <PDBx:citation_author citation_id="3" name="Darke, P.L."> <PDBx:ordinal>9</PDBx:ordinal> </PDBx:citation_author> <PDBx:citation_author citation_id="4" name="Darke, P.L."> <PDBx:ordinal>1</PDBx:ordinal> </PDBx:citation_author> <PDBx:citation_author citation_id="4" name="Leu, C.-T."> <PDBx:ordinal>2</PDBx:ordinal> </PDBx:citation_author> <PDBx:citation_author citation_id="4" name="Davis, L.J."> <PDBx:ordinal>3</PDBx:ordinal> </PDBx:citation_author> <PDBx:citation_author citation_id="4" name="Heimbach, J.C."> <PDBx:ordinal>4</PDBx:ordinal> </PDBx:citation_author> <PDBx:citation_author citation_id="4" name="Diehl, R.E."> <PDBx:ordinal>5</PDBx:ordinal> </PDBx:citation_author> <PDBx:citation_author citation_id="4" name="Hill, W.S."> <PDBx:ordinal>6</PDBx:ordinal> </PDBx:citation_author> <PDBx:citation_author citation_id="4" name="Dixon, R.A.F."> <PDBx:ordinal>7</PDBx:ordinal> </PDBx:citation_author> <PDBx:citation_author citation_id="4" name="Sigal, I.S."> <PDBx:ordinal>8</PDBx:ordinal> </PDBx:citation_author> </PDBx:citation_authorCategory> This data item defines the order of the author's name in the list of authors of a citation. This data item is a pointer to attribute id in category citation in the CITATION category. Name of an author of the citation; relevant for both journal articles and book chapters. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s). Bleary, Percival R. O'Neil, F.K. Van den Bossche, G. Yang, D.-L. Simonov, Yu.A Data items in the CITATION_EDITOR category record details about the editor associated with book chapter citations in the CITATION list. Example 1 - example is completely hypothetical <PDBx:citation_editorCategory> <PDBx:citation_editor citation_id="5" name="McKeever, B.M."></PDBx:citation_editor> <PDBx:citation_editor citation_id="5" name="Navia, M.A."></PDBx:citation_editor> <PDBx:citation_editor citation_id="5" name="Fitzgerald, P.M.D."></PDBx:citation_editor> <PDBx:citation_editor citation_id="5" name="Springer, J.P."></PDBx:citation_editor> </PDBx:citation_editorCategory> This data item defines the order of the editor's name in the list of editors of a citation. This data item is a pointer to attribute id in category citation in the CITATION category. Names of an editor of the citation; relevant for book chapters. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s). Bleary, Percival R. O'Neil, F.K. Van den Bossche, G. Yang, D.-L. Simonov, Yu.A Data items in the COMPUTING category record details about the computer programs used in the crystal structure analysis. Data items in this category would not, in general, be used in a macromolecular CIF. The category SOFTWARE, which allows for a more detailed description of computer programs and their attribues, would be used instead. Example 1 - Rodr\'iguez-Romera, Ruiz-P\'erez and Solans [(1996). Acta Cryst. C52, 1415-1417]. <PDBx:computingCategory> <PDBx:computing> <PDBx:data_collection>CAD-4 (Enraf-Nonius, 1989)</PDBx:data_collection> <PDBx:cell_refinement>CAD-4 (Enraf-Nonius, 1989)</PDBx:cell_refinement> <PDBx:data_reduction>CFEO (Solans, 1978)</PDBx:data_reduction> <PDBx:structure_solution>SHELXS86 (Sheldrick, 1990)</PDBx:structure_solution> <PDBx:structure_refinement>SHELXL93 (Sheldrick, 1993)</PDBx:structure_refinement> <PDBx:molecular_graphics>ORTEPII (Johnson, 1976)</PDBx:molecular_graphics> <PDBx:publication_material>PARST (Nardelli, 1983)</PDBx:publication_material> </PDBx:computing> </PDBx:computingCategory> Software used in refining the cell. Give the program or package name and a brief reference. CAD4 (Enraf-Nonius, 1989) Software used for data collection. Give the program or package name and a brief reference. CAD4 (Enraf-Nonius, 1989) Software used for data reduction. Give the program or package name and a brief reference. DIFDAT, SORTRF, ADDREF (XTAL3.0, 1990) Software used for molecular graphics. Give the program or package name and a brief reference. FRODO (Jones, 1986) & ORTEP (Johnson, 1965) Program/package name for data reduction/data scaling Program/package name for data reduction/intensity integration software Program/package name for structure refinement method. Software used for generating material for publication. Give the program or package name and a brief reference. Software used for refinement of the structure. Give the program or package name and a brief reference. SHELX85 (Sheldrick, 1985) X-PLOR (Brunger, 198?) Software used for solution of the structure. Give the program or package name and a brief reference. SHELX85 (Sheldrick, 1985) This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the DATABASE category have been superseded by data items in the DATABASE_2 category. They are included here only for compliance with older files. The code assigned by Chemical Abstracts. The code assigned by Cambridge Structural Database (organic and metal-organic compounds). The code assigned by the Inorganic Crystal Structure Data Base. The code assigned by the Metals Data File (metal structures). The code assigned by the NBS (NIST) Crystal Data Database (lattice parameters). The code assigned by the Powder Diffraction File (JCPDS/ICDD). The ASTM CODEN designator for a journal as given in the Chemical Source List maintained by the Chemical Astracts Service. The journal code used in the Cambridge Structural Database. This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the DATABASE_2 category record details about the database identifiers of the data block. These data items are assigned by database managers and should only appear in a data block if they originate from that source. The somewhat awkward name of this category (DATABASE_2) is a consequence of the name DATABASE having been already used in the CIF core, but used in a manner different from the usage in mmCIF. Since CIF data names, once adopted, cannot be changed, a new category was created. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:database_2Category> <PDBx:database_2 database_id="PDB" database_code="5HVP"></PDBx:database_2> </PDBx:database_2Category> An abbreviation that identifies the database. The code assigned by the database identified in attribute database_id in category database_2. 1ABC ABCDEF Data items in the DATABASE_PDB_CAVEAT category record details about features of the data block flagged as 'caveats' by the Protein Data Bank (PDB). These data items are included only for consistency with PDB format files. They should appear in a data block only if that data block was created by reformatting a PDB format file. Example 1 - completely hypothetical <PDBx:database_PDB_caveatCategory> <PDBx:database_PDB_caveat id="1"> <PDBx:text> CAVEAT 1ABC THE CRYSTAL TRANSFORMATION IS IN ERROR BUT IS</PDBx:text> </PDBx:database_PDB_caveat> <PDBx:database_PDB_caveat id="2"> <PDBx:text> CAVEAT 2 1ABC UNCORRECTABLE AT THIS TIME</PDBx:text> </PDBx:database_PDB_caveat> </PDBx:database_PDB_caveatCategory> The full text of the PDB caveat record. A unique identifier for the PDB caveat record. The DATABASE_PDB_MATRIX category provides placeholders for transformation matrices and vectors used by the Protein Data Bank (PDB). These data items are included only for consistency with older PDB format files. They should appear in a data block only if that data block was created by reformatting a PDB format file. The [1][1] element of the PDB ORIGX matrix. The [1][2] element of the PDB ORIGX matrix. The [1][3] element of the PDB ORIGX matrix. The [2][1] element of the PDB ORIGX matrix. The [2][2] element of the PDB ORIGX matrix. The [2][3] element of the PDB ORIGX matrix. The [3][1] element of the PDB ORIGX matrix. The [3][2] element of the PDB ORIGX matrix. The [3][3] element of the PDB ORIGX matrix. The [1] element of the PDB ORIGX vector. The [2] element of the PDB ORIGX vector. The [3] element of the PDB ORIGX vector. The [1][1] element of the PDB SCALE matrix. The [1][2] element of the PDB SCALE matrix. The [1][3] element of the PDB SCALE matrix. The [2][1] element of the PDB SCALE matrix. The [2][2] element of the PDB SCALE matrix. The [2][3] element of the PDB SCALE matrix. The [3][1] element of the PDB SCALE matrix. The [3][2] element of the PDB SCALE matrix. The [1][1] element of the PDB SCALE matrix. The [1] element of the PDB SCALE vector. The [2] element of the PDB SCALE vector. The [3] element of the PDB SCALE vector. This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the DATABASE_PDB_REMARK category record details about the data block as archived by the Protein Data Bank (PDB). Some data appearing in PDB REMARK records can be algorithmically extracted into the appropriate data items in the data block. These data items are included only for consistency with older PDB format files. They should appear in a data block only if that data block was created by reformatting a PDB format file. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:database_PDB_remarkCategory> <PDBx:database_PDB_remark id="3"> <PDBx:text> REMARK 3 5HVP REMARK 3 REFINEMENT. BY THE RESTRAINED LEAST-SQUARES PROCEDURE OF J. 5HVP REMARK 3 KONNERT AND W. HENDRICKSON (PROGRAM *PROLSQ*). THE R 5HVP REMARK 3 VALUE IS 0.176 FOR 12901 REFLECTIONS IN THE RESOLUTION 5HVP REMARK 3 RANGE 8.0 TO 2.0 ANGSTROMS WITH I .GT. SIGMA(I). 5HVP REMARK 3 5HVP REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES (THE VALUES OF 5HVP REMARK 3 SIGMA, IN PARENTHESES, ARE THE INPUT ESTIMATED 5HVP REMARK 3 STANDARD DEVIATIONS THAT DETERMINE THE RELATIVE 5HVP REMARK 3 WEIGHTS OF THE CORRESPONDING RESTRAINTS) 5HVP REMARK 3 DISTANCE RESTRAINTS (ANGSTROMS) 5HVP REMARK 3 BOND DISTANCE 0.018(0.020) 5HVP REMARK 3 ANGLE DISTANCE 0.038(0.030) 5HVP REMARK 3 PLANAR 1-4 DISTANCE 0.043(0.040) 5HVP REMARK 3 PLANE RESTRAINT (ANGSTROMS) 0.015(0.020) 5HVP REMARK 3 CHIRAL-CENTER RESTRAINT (ANGSTROMS**3) 0.177(0.150) 5HVP REMARK 3 NON-BONDED CONTACT RESTRAINTS (ANGSTROMS) 5HVP REMARK 3 SINGLE TORSION CONTACT 0.216(0.500) 5HVP REMARK 3 MULTIPLE TORSION CONTACT 0.207(0.500) 5HVP REMARK 3 POSSIBLE HYDROGEN BOND 0.245(0.500) 5HVP REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINT (DEGREES) 5HVP REMARK 3 PLANAR (OMEGA) 2.6(3.0) 5HVP REMARK 3 STAGGERED 17.4(15.0) 5HVP REMARK 3 ORTHONORMAL 18.1(20.0) 5HVP</PDBx:text> </PDBx:database_PDB_remark> <PDBx:database_PDB_remark id="4"> <PDBx:text> REMARK 4 5HVP REMARK 4 THE TWO CHAINS OF THE DIMERIC ENZYME HAS BEEN ASSIGNED THE 5HVP REMARK 4 THE CHAIN INDICATORS *A* AND *B*. 5HVP</PDBx:text> </PDBx:database_PDB_remark> </PDBx:database_PDB_remarkCategory> The full text of the PDB remark record. A unique identifier for the PDB remark record. Data items in the DATABASE_PDB_REV category record details about the history of the data block as archived by the Protein Data Bank (PDB). These data items are assigned by the PDB database managers and should only appear in a data block if they originate from that source. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:database_PDB_revCategory> <PDBx:database_PDB_rev num="1"> <PDBx:author_name>Fitzgerald, Paula M.D</PDBx:author_name> <PDBx:date>1991-10-15</PDBx:date> <PDBx:date_original>1990-04-30</PDBx:date_original> <PDBx:status>full release</PDBx:status> <PDBx:mod_type>0</PDBx:mod_type> </PDBx:database_PDB_rev> </PDBx:database_PDB_revCategory> The name of the person responsible for submitting this revision to the PDB. The family name(s) followed by a comma, precedes the first name(s) or initial(s). Bleary, Percival R. O'Neil, F.K. Van den Bossche, G. Yang, D.-L. Simonov, Yu.A Date the PDB revision took place. Taken from the REVDAT record. Date the entry first entered the PDB database in the form: yyyy-mm-dd. Taken from the PDB HEADER record. 1980-08-21 Taken from the REVDAT record. Refer to the Protein Data Bank format description for details. The PDB code for a subsequent PDB entry that replaced the PDB file corresponding to this data block. The PDB code for a previous PDB entry that was replaced by the PDB file corresponding to this data block. The status of this revision. The value of attribute num in category database_PDB_rev must uniquely and sequentially identify a record in the DATABASE_PDB_REV list. Note that this item must be a number, and that modification numbers are assigned in increasing numerical order. Data items in the DATABASE_PDB_REV_RECORD category record details about specific record types that were changed in a given revision of a PDB entry. These data items are assigned by the PDB database managers and should only appear in a data block if they originate from that source. Example 1 - example is completely hypothetical <PDBx:database_PDB_rev_recordCategory> <PDBx:database_PDB_rev_record rev_num="1" type="CONECT"> <PDBx:details>Error fix - incorrect connection between atoms 2312 and 2317</PDBx:details> </PDBx:database_PDB_rev_record> <PDBx:database_PDB_rev_record rev_num="2" type="MATRIX"> <PDBx:details>For consistency with 1995-08-04 style-guide</PDBx:details> </PDBx:database_PDB_rev_record> <PDBx:database_PDB_rev_record rev_num="3" type="ORIGX"> <PDBx:details>Based on new data from author</PDBx:details> </PDBx:database_PDB_rev_record> </PDBx:database_PDB_rev_recordCategory> A description of special aspects of the revision of records in this PDB entry. Based on new data from author For consistency with 1995-08-04 style-guide For consistency with structural class This data item is a pointer to attribute num in category database_PDB_rev in the DATABASE_PDB_REV category. The types of records that were changed in this revision to a PDB entry. CRYST1 SCALE MTRIX ATOM HETATM The DATABASE_PDB_TVECT category provides placeholders for the TVECT matrices and vectors used by the Protein Data Bank (PDB). These data items are included only for consistency with older PDB format files. They should appear in a data block only if that data block was created by reformatting a PDB format file. A description of special aspects of this TVECT. The [1] element of the PDB TVECT vector. The [2] element of the PDB TVECT vector. The [3] element of the PDB TVECT vector. The value of attribute id in category database_PDB_tvect must uniquely identify a record in the DATABASE_PDB_TVECT list. Note that this item need not be a number; it can be any unique identifier. Data items in the DIFFRN category record details about the diffraction data and its measurement. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:diffrnCategory> <PDBx:diffrn id="Set1"> <PDBx:ambient_temp>293(3)</PDBx:ambient_temp> <PDBx:ambient_environment> Mother liquor from the reservoir of the vapor diffusion experiment, mounted in room air</PDBx:ambient_environment> <PDBx:crystal_support> 0.7 mm glass capillary, sealed with dental wax</PDBx:crystal_support> <PDBx:crystal_treatment> Equilibrated in rotating anode radiation enclosure for 18 hours prior to beginning of data collection.</PDBx:crystal_treatment> </PDBx:diffrn> </PDBx:diffrnCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. <PDBx:diffrnCategory> <PDBx:diffrn id="d1"> <PDBx:details> \q scan width (1.0 + 0.14tan\q)\&#37;, \q scan rate 1.2\&#37; per min. Background counts for 5 sec on each side every scan.</PDBx:details> <PDBx:ambient_temp>293</PDBx:ambient_temp> </PDBx:diffrn> </PDBx:diffrnCategory> The gas or liquid surrounding the sample, if not air. The mean pressure in kilopascals at which the intensities were measured. The estimated standard deviation of attribute ambient_pressure in category diffrn. The mean temperature in kelvins at which the intensities were measured. A description of special aspects of temperature control during data collection. The estimated standard deviation of attribute ambient_temp in category diffrn. This data item is a pointer to attribute id in category exptl_crystal in the EXPTL_CRYSTAL category. The physical device used to support the crystal during data collection. glass capillary quartz capillary fiber metal loop Remarks about how the crystal was treated prior to intensity measurement. Particularly relevant when intensities were measured at low temperature. equilibrated in hutch for 24 hours flash frozen in liquid nitrogen slow cooled with direct air stream Special details of the diffraction measurement process. Should include information about source instability, crystal motion, degradation and so on. This data item uniquely identifies a set of diffraction data. Data items in the DIFFRN_ATTENUATOR category record details about the diffraction attenuator scales employed. Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. <PDBx:diffrn_attenuatorCategory> <PDBx:diffrn_attenuator code="1"> <PDBx:scale>16.976</PDBx:scale> </PDBx:diffrn_attenuator> </PDBx:diffrn_attenuatorCategory> The scale factor applied when an intensity measurement is reduced by an attenuator identified by attribute in category diffrn_attenuator_code This scale must be multiplied by the measured intensity to convert it to the same scale as unattenuated intensities. A code associated with a particular attenuator setting. This code is referenced by the attribute attenuator_code in category diffrn_refln which is stored with the diffraction data. See attribute scale in category diffrn_attenuator. Data items in the DIFFRN_DETECTOR category describe the detector used to measure the scattered radiation, including any analyser and post-sample collimation. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:diffrn_detectorCategory> <PDBx:diffrn_detector diffrn_id="d1"> <PDBx:detector>multiwire</PDBx:detector> <PDBx:type>Siemens</PDBx:type> </PDBx:diffrn_detector> </PDBx:diffrn_detectorCategory> A description of special aspects of the radiation detector. Need new example here. The general class of the radiation detector. photographic film scintillation counter CCD plate BF~3~ counter The deadtime in microseconds of the detectors used to measure the diffraction intensities. The date of data collection. 1996-12-25 The make, model or name of the detector device used. This data item is a pointer to attribute id in category diffrn in the DIFFRN category. Data items in the DIFFRN_MEASUREMENT category record details about the device used to orient and/or position the crystal during data measurement and the manner in which the diffraction data were measured. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:diffrn_measurementCategory> <PDBx:diffrn_measurement diffrn_id="d1"> <PDBx:device>3-circle camera</PDBx:device> <PDBx:device_type>Supper model x</PDBx:device_type> <PDBx:device_details>none</PDBx:device_details> <PDBx:method>omega scan</PDBx:method> <PDBx:details> 440 frames, 0.20 degrees, 150 sec, detector distance 12 cm, detector angle 22.5 degrees</PDBx:details> </PDBx:diffrn_measurement> </PDBx:diffrn_measurementCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. <PDBx:diffrn_measurementCategory> <PDBx:diffrn_measurement diffrn_id="s1"> <PDBx:device_type>Philips PW1100/20 diffractometer</PDBx:device_type> <PDBx:method>\q/2\q</PDBx:method> </PDBx:diffrn_measurement> </PDBx:diffrn_measurementCategory> A description of special aspects of the intensity measurement. 440 frames, 0.20 degrees, 150 sec, detector distance 12 cm, detector angle 22.5 degrees The general class of goniometer or device used to support and orient the specimen. 3-circle camera 4-circle camera kappa-geometry camera oscillation camera precession camera A description of special aspects of the device used to measure the diffraction intensities. Need new example here. The make, model or name of the measurement device (goniometer) used. Supper model q Huber model r Enraf-Nonius model s homemade Method used to measure intensities. profile data from theta/2theta scans The physical device used to support the crystal during data collection. glass capillary quartz capillary fiber metal loop This data item is a pointer to attribute id in category diffrn in the DIFFRN category. Data items in the DIFFRN_ORIENT_MATRIX category record details about the orientation matrix used in data measurement. Example 1 - based on CAD-4 diffractometer data obtained for Yb(S-C5H4N)2 (THF)4 <PDBx:diffrn_orient_matrixCategory> <PDBx:diffrn_orient_matrix diffrn_id="set1"> <PDBx:type> reciprocal axis matrix, multiplies hkl vector to generate diffractometer xyz vector and diffractometer angles</PDBx:type> <PDBx:UB11>-0.071479</PDBx:UB11> <PDBx:UB12>0.020208</PDBx:UB12> <PDBx:UB13>0.039076</PDBx:UB13> <PDBx:UB21>0.035372</PDBx:UB21> <PDBx:UB22>0.056209</PDBx:UB22> <PDBx:UB23>0.078324</PDBx:UB23> <PDBx:UB31>-0.007470</PDBx:UB31> <PDBx:UB32>0.067854</PDBx:UB32> <PDBx:UB33>-0.017832</PDBx:UB33> </PDBx:diffrn_orient_matrix> </PDBx:diffrn_orient_matrixCategory> The [1][1] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation to the local diffractometer axes. See also attribute type in category diffrn_orient_matrix. The [1][2] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation to the local diffractometer axes. See also attribute type in category diffrn_orient_matrix. The [1][3] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation to the local diffractometer axes. See also attribute type in category diffrn_orient_matrix. The [2][1] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation to the local diffractometer axes. See also attribute type in category diffrn_orient_matrix. The [2][2] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation to the local diffractometer axes. See also attribute type in category diffrn_orient_matrix. The [2][3] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation to the local diffractometer axes. See also attribute type in category diffrn_orient_matrix. The [3][1] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation to the local diffractometer axes. See also attribute type in category diffrn_orient_matrix. The [3][2] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation to the local diffractometer axes. See also attribute type in category diffrn_orient_matrix. The [3][3] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation to the local diffractometer axes. See also attribute type in category diffrn_orient_matrix. A description of the orientation matrix type and how it should be applied to define the orientation of the crystal precisely with respect to the diffractometer axes. This data item is a pointer to attribute id in category diffrn in the DIFFRN category. Data items in the DIFFRN_ORIENT_REFLN category record details about the reflections that define the orientation matrix used in measurement of diffraction intensities. Example 1 - based on CAD-4 diffractometer data obtained for Yb(S-C5H4N)2 (THF)4 <PDBx:diffrn_orient_reflnCategory> <PDBx:diffrn_orient_refln diffrn_id="myset1" index_h="2" index_k="0" index_l="2"> <PDBx:angle_chi>-28.45</PDBx:angle_chi> <PDBx:angle_kappa>-11.32</PDBx:angle_kappa> <PDBx:angle_omega>5.33</PDBx:angle_omega> <PDBx:angle_phi>101.78</PDBx:angle_phi> <PDBx:angle_psi>0.00</PDBx:angle_psi> <PDBx:angle_theta>10.66</PDBx:angle_theta> </PDBx:diffrn_orient_refln> </PDBx:diffrn_orient_reflnCategory> Diffractometer angle chi in degrees of a reflection used to define the orientation matrix. See attribute UB in category diffrn_orient_matrix and the Miller indices in the DIFFRN_ORIENT_REFLN category. Diffractometer angle kappa in degrees of a reflection used to define the orientation matrix. See attribute UB in category diffrn_orient_matrix and the Miller indices in the DIFFRN_ORIENT_REFLN category. Diffractometer angle omega in degrees of a reflection used to define the orientation matrix. See attribute UB in category diffrn_orient_matrix and the Miller indices in the DIFFRN_ORIENT_REFLN category. Diffractometer angle phi in degrees of a reflection used to define the orientation matrix. See attribute UB in category diffrn_orient_matrix and the Miller indices in the DIFFRN_ORIENT_REFLN category. Diffractometer angle psi in degrees of a reflection used to define the orientation matrix. See attribute UB in category diffrn_orient_matrix and the Miller indices in the DIFFRN_ORIENT_REFLN category. Diffractometer angle theta in degrees of a reflection used to define the orientation matrix. See attribute UB in category diffrn_orient_matrix and the Miller indices in the DIFFRN_ORIENT_REFLN category. This data item is a pointer to attribute id in category diffrn in the DIFFRN category. Miller index h of a reflection used to define the orientation matrix. Miller index k of a reflection used to define the orientation matrix. Miller index l of a reflection used to define the orientation matrix. Data items in the DIFFRN_RADIATION category describe the radiation used in measuring diffraction intensities, its collimation and monochromatisation before the sample. Post-sample treatment of the beam is described by data items in the DIFFRN_DETECTOR category. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:diffrn_radiationCategory> <PDBx:diffrn_radiation diffrn_id="set1"> <PDBx:collimation>0.3 mm double pinhole</PDBx:collimation> <PDBx:monochromator>graphite</PDBx:monochromator> <PDBx:type>Cu K\a</PDBx:type> <PDBx:wavelength_id>1</PDBx:wavelength_id> </PDBx:diffrn_radiation> </PDBx:diffrn_radiationCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. <PDBx:diffrn_radiationCategory> <PDBx:diffrn_radiation> <PDBx:wavelength_id>1</PDBx:wavelength_id> <PDBx:type>Cu K\a</PDBx:type> <PDBx:monochromator>graphite</PDBx:monochromator> </PDBx:diffrn_radiation> </PDBx:diffrn_radiationCategory> The collimation or focusing applied to the radiation. 0.3 mm double-pinhole 0.5 mm focusing mirrors Absorption edge in angstroms of the radiation filter used. Half-width in millimetres of the incident beam in the direction perpendicular to the diffraction plane. The method used to obtain monochromatic radiation. If a mono- chromator crystal is used the material and the indices of the Bragg reflection are specified. Zr filter Ge 220 none equatorial mounted graphite SINGLE WAVELENGTH, LAUE, or MAD. SINGLE WAVELENGTH MONOCHROMATIC LAUE MAD OTHER Monochromatic or Laue. M L Wavelength of radiation. Comma separated list of wavelengths or wavelength range. The angle in degrees, as viewed from the specimen, between the perpendicular component of the polarisation and the diffraction plane. See attribute in category diffrn_radiation_polarisn_ratio. Polarisation ratio of the diffraction beam incident on the crystal. It is the ratio of the perpendicularly polarised to the parallel polarised component of the radiation. The perpendicular component forms an angle of attribute polarisn_norm in category diffrn_radiation to the normal to the diffraction plane of the sample (i.e. the plane containing the incident and reflected beams). Name of the type of radiation used. It is strongly encouraged that this field be specified so that the probe radiation can be simply determined. The nature of the radiation. This is typically a description of the X-ray wavelength in Siegbahn notation. CuK\a Cu K\a~1~ Cu K-L~2,3~ white-beam This data item is a pointer to attribute id in category diffrn_radiation_wavelength in the DIFFRN_RADIATION_WAVELENGTH category. The IUPAC symbol for the X-ray wavelength for probe radiation. This data item is a pointer to attribute id in category diffrn in the DIFFRN category. Data items in the DIFFRN_RADIATION_WAVELENGTH category describe the wavelength of radiation used in measuring diffraction intensities. Items may be looped to identify and assign weights to distinct components of a polychromatic beam. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:diffrn_radiation_wavelengthCategory> <PDBx:diffrn_radiation_wavelength id="1"> <PDBx:wavelength>1.54</PDBx:wavelength> <PDBx:wt>1.0</PDBx:wt> </PDBx:diffrn_radiation_wavelength> </PDBx:diffrn_radiation_wavelengthCategory> The radiation wavelength in angstroms. The relative weight of a wavelength identified by the code attribute id in category diffrn_radiation_wavelength in the list of wavelengths. The code identifying each value of attribute in category diffrn_radiation_wavelength Items in the DIFFRN_RADIATION_WAVELENGTH category are looped when multiple wavelengths are used. This code is used to link with the DIFFRN_REFLN category. The attribute wavelength_id in category diffrn_refln codes must match one of the codes defined in this category. x1 x2 neut Data items in the DIFFRN_REFLN category record details about the intensities measured in the diffraction data set identified by attribute diffrn_id. in category diffrn_refln The DIFFRN_REFLN data items refer to individual intensity measurements, and must be included in looped lists. The DIFFRN_REFLNS data items specify the parameters that apply to all intensity measurements in the particular diffraction data set identified by attribute diffrn_id in category diffrn_reflns. Example 1 - based on CAD-4 diffractometer data obtained for Yb(S-C5H4N)2 (THF)4 for data set 'set1' reflection 1102 <PDBx:diffrn_reflnCategory> <PDBx:diffrn_refln diffrn_id="set1" id="1102"> <PDBx:wavelength_id>Cu1fixed</PDBx:wavelength_id> <PDBx:angle_chi>32.21</PDBx:angle_chi> <PDBx:angle_kappa>20.12</PDBx:angle_kappa> <PDBx:angle_omega>11.54</PDBx:angle_omega> <PDBx:angle_phi>176.02</PDBx:angle_phi> <PDBx:angle_psi>0.00</PDBx:angle_psi> <PDBx:angle_theta>23.08</PDBx:angle_theta> <PDBx:attenuator_code>Ni.005</PDBx:attenuator_code> <PDBx:counts_bg_1>22</PDBx:counts_bg_1> <PDBx:counts_bg_2>25</PDBx:counts_bg_2> <PDBx:counts_net>3450</PDBx:counts_net> <PDBx:counts_peak>321</PDBx:counts_peak> <PDBx:counts_total>3499</PDBx:counts_total> <PDBx:detect_slit_horiz>0.04</PDBx:detect_slit_horiz> <PDBx:detect_slit_vert>0.02</PDBx:detect_slit_vert> <PDBx:elapsed_time>1.00</PDBx:elapsed_time> <PDBx:index_h>4</PDBx:index_h> <PDBx:index_k>0</PDBx:index_k> <PDBx:index_l>2</PDBx:index_l> <PDBx:intensity_net>202.56</PDBx:intensity_net> <PDBx:intensity_sigma>2.18</PDBx:intensity_sigma> <PDBx:scale_group_code>A24</PDBx:scale_group_code> <PDBx:scan_mode>om</PDBx:scan_mode> <PDBx:scan_mode_backgd>mo</PDBx:scan_mode_backgd> <PDBx:scan_rate>1.2</PDBx:scan_rate> <PDBx:scan_time_backgd>900.00</PDBx:scan_time_backgd> <PDBx:scan_width>1.0</PDBx:scan_width> <PDBx:sint_over_lambda>0.25426</PDBx:sint_over_lambda> <PDBx:standard_code>1</PDBx:standard_code> <PDBx:wavelength>1.54184</PDBx:wavelength> </PDBx:diffrn_refln> </PDBx:diffrn_reflnCategory> The diffractometer angle chi in degrees of a reflection. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. The diffractometer angle kappa in degrees of a reflection. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. The diffractometer angle omega in degrees of a reflection. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. The diffractometer angle phi in degrees of a reflection. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. The diffractometer angle psi in degrees of a reflection. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. The diffractometer angle theta in degrees of a reflection. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. The code identifying the attenuator setting for this reflection. This code must match one of the attribute code in category diffrn_attenuator values. The diffractometer counts for the measurement of the background before the peak. The diffractometer counts for the measurement of the background after the peak. The diffractometer counts for the measurement of net counts after background removal. The diffractometer counts for the measurement of counts for the peak scan or position. The diffractometer counts for the measurement of total counts (background plus peak). Total slit aperture in degrees in the diffraction plane. Total slit aperture in degrees perpendicular to the diffraction plane. Elapsed time in minutes from the start of diffraction measurement to the measurement of this intensity. Miller index h of a diffraction reflection. The values of the Miller indices in the DIFFRN_REFLN category need not match the values of the Miller indices in the REFLN category if a transformation of the original measured cell has taken place. Details of the cell transformation are described in attribute reduction_process in category diffrn_reflns. See also attribute transf_matrix in category diffrn_reflns. Miller index k of a diffraction reflection. The values of the Miller indices in the DIFFRN_REFLN category need not match the values of the Miller indices in the REFLN category if a transformation of the original measured cell has taken place. Details of the cell transformation are described in attribute reduction_process in category diffrn_reflns. See also attribute transf_matrix in category diffrn_reflns. Miller index l of a diffraction reflection. The values of the Miller indices in the DIFFRN_REFLN category need not match the values of the Miller indices in the REFLN category if a transformation of the original measured cell has taken place. Details of the cell transformation are described in attribute reduction_process in category diffrn_reflns. See also attribute transf_matrix in category diffrn_reflns. Net intensity calculated from the diffraction counts after the attenuator and standard scales have been applied. Standard uncertainty (e.s.d.) of the intensity calculated from the diffraction counts after the attenuator and standard scales have been applied. The code identifying the scale applying to this reflection. This data item is a pointer to attribute code in category diffrn_scale_group in the DIFFRN_SCALE_GROUP category. The code identifying the mode of scanning with a diffractometer. See _diffrn_refln.scan_width and _diffrn_refln.scan_mode_backgd. The code identifying the mode of scanning a reflection to measure the background intensity. The rate of scanning a reflection to measure the intensity in degrees per minute. The time spent measuring each background in seconds. The scan width in degrees of the scan mode defined by the code attribute scan_mode in category diffrn_refln. The (sin theta)/lambda value in reciprocal angstroms for this reflection. The code identifying that this reflection was measured as a standard intensity. This data item is a pointer to attribute code in category diffrn_standard_refln in the DIFFRN_STANDARD_REFLN category. The mean wavelength in angstroms of radiation used to measure the intensity of this reflection. This is an important parameter for data collected using energy dispersive detectors or the Laue method. This data item is a pointer to attribute wavelength_id in category diffrn_radiation in the DIFFRN_RADIATION category. This data item is a pointer to attribute id in category diffrn in the DIFFRN category. The value of diffrn_refln.id must uniquely identify the reflection in the data set identified by the item attribute diffrn_id. in category diffrn_refln Note that this item need not be a number; it can be any unique identifier. Data items in the DIFFRN_REFLNS category record details about the set of intensities measured in the diffraction experiment. The DIFFRN_REFLN data items refer to individual intensity measurements, and must be included in looped lists. The DIFFRN_REFLNS data items specify the parameters that apply to all intensity measurements in a diffraction data set. The residual [sum|avdel(I)| / sum|av(I)|] for symmetry-equivalent reflections used to calculate the average intensity av(I). The avdel(I) term is the average difference between av(I) and the individual symmetry-equivalent intensities. Measure [sum|sigma(I)|/sum|net(I)|] for all measured reflections. The maximum value of the diffraction reflection data specified by attribute index_h in category diffrn_refln. The minimum value of the diffraction reflection data specified by attribute index_h in category diffrn_refln. The maximum value of the diffraction reflection data specified by attribute index_k in category diffrn_refln. The minimum value of the diffraction reflection data specified by attribute index_k in category diffrn_refln. The maximum value of the diffraction reflection data specified by attribute index_l in category diffrn_refln. The minimum value of the diffraction reflection data specified by attribute index_l in category diffrn_refln. The total number of measured intensities, excluding reflections that are classified as systematically absent. A description of the process used to reduce the intensity data into structure-factor magnitudes. data averaged using Fisher test Maximum theta angle in degrees for the measured diffraction intensities. Minimum theta angle in degrees for the measured diffraction intensities. The [1][1] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. The [1][2] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. The [1][3] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. The [2][1] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. The [2][2] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. The [2][3] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. The [3][1] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. The [3][2] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. The [3][3] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. This data item is a pointer to attribute id in category diffrn in the DIFFRN category. Data items in the DIFFRN_SCALE_GROUP category record details about the reflections used to scale the diffraction intensities. Scaling groups might, for instance, correspond to each film in a multi-film data set, or each crystal in a multi-crystal data set. Example 1 - based on CAD-4 diffractometer data obtained for Yb(S-C5H4N)2 (THF)4 <PDBx:diffrn_scale_groupCategory> <PDBx:diffrn_scale_group code="A24"> <PDBx:I_net>1.021</PDBx:I_net> </PDBx:diffrn_scale_group> </PDBx:diffrn_scale_groupCategory> The scale for a specific measurement group which is to be multiplied with the net intensity to place all intensities in the DIFFRN_REFLN or REFLN list on a common scale. The value of diffrn_scale_group.code must uniquely identify a record in the DIFFRN_SCALE_GROUP list. Note that this item need not be a number; it can be any unique identifier. 1 2 c1 c2 Data items in the DIFFRN_SOURCE category record details of the source of radiation used in the diffraction experiment. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:diffrn_sourceCategory> <PDBx:diffrn_source diffrn_id="s1"> <PDBx:source>rotating anode</PDBx:source> <PDBx:type>Rigaku RU-200</PDBx:type> <PDBx:power>50kw,180mA</PDBx:power> <PDBx:target>8mm x 0.4 mm broad-focus</PDBx:target> </PDBx:diffrn_source> </PDBx:diffrn_sourceCategory> The current in milliamperes at which the radiation source was operated. A description of special aspects of the radiation source used. Synchrotron beamline. Synchrotron site. The power in kilowatts at which the radiation source was operated. The dimensions of the source as viewed from the sample. 8mm x 0.4 mm fine-focus broad focus The general class of the radiation source. sealed X-ray tube nuclear reactor spallation source electron microscope rotating-anode X-ray tube synchrotron The chemical element symbol for the X-ray target (usually the anode) used for generation of X-rays. This can be used also for spallation sources. The make, model or name of the source of radiation. NSLS beamline X8C Rigaku RU200 The voltage in kilovolts at which the radiation source was operated. This data item is a pointer to attribute id in category diffrn in the DIFFRN category. Data items in the DIFFRN_STANDARD_REFLN category record details about the reflections treated as standards during the measurement of a set of diffraction intensities. Note that these are the individual standard reflections, not the results of the analysis of the standard reflections. Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. <PDBx:diffrn_standard_reflnCategory> <PDBx:diffrn_standard_refln diffrn_id="s1" code="1"> <PDBx:index_h>3</PDBx:index_h> <PDBx:index_k>2</PDBx:index_k> <PDBx:index_l>4</PDBx:index_l> </PDBx:diffrn_standard_refln> <PDBx:diffrn_standard_refln diffrn_id="s1" code="1"> <PDBx:index_h>1</PDBx:index_h> <PDBx:index_k>9</PDBx:index_k> <PDBx:index_l>1</PDBx:index_l> </PDBx:diffrn_standard_refln> <PDBx:diffrn_standard_refln diffrn_id="s1" code="1"> <PDBx:index_h>3</PDBx:index_h> <PDBx:index_k>0</PDBx:index_k> <PDBx:index_l>10</PDBx:index_l> </PDBx:diffrn_standard_refln> </PDBx:diffrn_standard_reflnCategory> Miller index h of a standard reflection used in the diffraction measurement process. Miller index k of a standard reflection used in the diffraction measurement process. Miller index l of a standard reflection used in the diffraction measurement process. This data item is a pointer to attribute id in category diffrn in the DIFFRN category. The code identifying a reflection measured as a standard reflection with the indices attribute index_h, in category diffrn_standard_refln attribute index_k in category diffrn_standard_refln and attribute index_l in category diffrn_standard_refln. This is the same code as the attribute standard_code in category diffrn_refln in the DIFFRN_REFLN list. 1 2 c1 c2 Data items in the DIFFRN_STANDARDS category record details about the set of standard reflections used to monitor intensity stability during measurement of diffraction intensities. Note that these records describe properties common to the set of standard reflections, not the standard reflections themselves. Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. <PDBx:diffrn_standardsCategory> <PDBx:diffrn_standards diffrn_id="s1"> <PDBx:number>3</PDBx:number> <PDBx:interval_time>120</PDBx:interval_time> <PDBx:decay_>0</PDBx:decay_> </PDBx:diffrn_standards> </PDBx:diffrn_standardsCategory> The percentage decrease in the mean of the intensities for the set of standard reflections at the start of the measurement process and at the finish. This value usually affords a measure of the overall decay in crystal quality during the diffraction measurement process. Negative values are used in exceptional instances where the final intensities are greater than the initial ones. The number of reflection intensities between the measurement of standard reflection intensities. The time in minutes between the measurement of standard reflection intensities. The number of unique standard reflections used in the diffraction measurements. The standard uncertainty (e.s.d.) of the individual mean standard scales applied to the intensity data. This data item is a pointer to attribute id in category diffrn in the DIFFRN category. Data items in the EM_2D_CRYSTAL_GROW category record details of growth conditions for 2d crystal samples. Example 1 - based on PDB entry 1AT9 and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_2d_crystal_growCategory> <PDBx:em_2d_crystal_grow id="1"> <PDBx:atmosphere>room air</PDBx:atmosphere> <PDBx:pH>5.2</PDBx:pH> <PDBx:temp>18</PDBx:temp> <PDBx:buffer_id>2</PDBx:buffer_id> <PDBx:details>on grid</PDBx:details> <PDBx:number_2d_crystals>129</PDBx:number_2d_crystals> <PDBx:citation_id>2</PDBx:citation_id> </PDBx:em_2d_crystal_grow> </PDBx:em_2d_crystal_growCategory> The type of the apparatus used for growing the crystals. Langmuir trough The type of atmosphere in which crystals were grown. room air This data item is a pointer to attribute id in category em_buffer in the BUFFER category. This data item is a pointer to attribute id in category citation in the CITATION category. Any additional items concerning 2d crystal growth. The approximate size (microns squared) of 2d crystals imaged. The method used for growing the crystals. lipid monolayer The number of 2d crystals imaged. the pH value used for growing the crystals. 4.7 The value of the temperature in degrees Kelvin used for growing the crystals. 293 The length of time required to grow the crystals. approximately 2 days The value of attribute crystal_id in category em_2d_crystal_grow must uniquely identify the sample 2d crystal. Data items in the EM_2D_PROJECTION_SELECTION category record details of images from scanned micrographs and the number of particles selected from a scanned set of micrographs. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_2d_projection_selectionCategory> <PDBx:em_2d_projection_selection entry_id="1"> <PDBx:software_name>1</PDBx:software_name> <PDBx:method>INTERACTIVE</PDBx:method> <PDBx:citation_id>1</PDBx:citation_id> </PDBx:em_2d_projection_selection> </PDBx:em_2d_projection_selectionCategory> This data item is a pointer to attribute id in category citation in the CITATION category. Any additional details used for selecting observed assemblies. negative monitor contrast facilitated particle picking The method used for selecting observed assemblies. particles picked interactively from monitor The number of particles selected from the projection set of images. 840 This data item is a pointer to attribute name in category software in the SOFTWARE category. The value of attribute entry_id in category em_2d_projection_selection points to the ENTRY category. Data items in the 3D_FITTING category record details of the method of fitting atomic coordinates from a PDB file into a 3d-em volume map file Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_3d_fittingCategory> <PDBx:em_3d_fitting id="1" entry_id="1DYL"> <PDBx:method>AUTOMATIC</PDBx:method> <PDBx:target_criteria>R-FACTOR</PDBx:target_criteria> <PDBx:software_name>1</PDBx:software_name> <PDBx:ref_space>REAL</PDBx:ref_space> <PDBx:ref_protocol>RIGID BODY REFINEMENT</PDBx:ref_protocol> <PDBx:details> THE CRYSTAL STRUCTURE OF THE CAPSID PROTEIN FROM CHOI ET AL (1997) PROTEINS 3 27:345-359 (SUBUNIT A OF PDB FILE 1VCQ) WAS PLACED INTO THE CRYO-EM DENSITY MAP. THE CAPSID PROTEIN WAS FIRST MANUALLY POSITIONED INTO THE CRYO-EM DENSITY CORRESPONDING TO POSITIONS OF THE FOUR INDEPENDENT MONOMER DENSITIES BETWEEN THE INNER LEAFLET OF THE BILAYER AND THE RNA. THESE POSITIONS WERE THEN REFINED BY RIGID BODY REFINEMENT IN REAL SPACE WITH THE PROGRAM EMFIT (CHENG ET AL. 1995, CELL 80, 621-630). THE QUALITY OF THE FIT CAN BE SEEN FROM THE MAP DENSITY WITHIN THE PROTEIN. ALL 4563 ATOMS ARE IN DENSITY OF AT LEAST 4 SIGMA (96.73) ABOVE THE AVERAGE (512.04), 1167 ATOMS ARE IN DENSITY BETWEEN 4 AND 5 SIGMA, 3174 ATOMS ARE IN DENSITY BETWEEN 5 AND 6 SIGMA, AND 222 ATOMS ARE IN DENSTY OF 6 SIGMA OR ABOVE. THE VARIATION IN DENSITY OVER THE FITTED PROTEIN CAN BE VISUALIZED WITH THE PSEUDO TEMPERATURE FACTOR. THE DENSITY VALUE AT EACH ATOM IS GIVEN IN THE 8TH COLUM (USUALLY THE OCCUPANCY) AS THE NUMBER OF STANDARD DEVIATION ABOVE BACKGROUND. COLUMN NINE (USUALLY THE TEMPERATURE FACTOR) CONTAINS THE VALUE OF THE RELATIVE DENSITY WITHIN THE FITTED PROTEIN SCALED LINEARLY SO THAT THE MINIMUM DENSITY IS 100.0 AND THE MAXIMUM DENSITY IS 1.0. THE ATOMS THAT LIE IN THE LOWER DENSITY REGIONS WILL HAVE THE HIGHEST PSEUDO TEMPERATURE FACTORS. </PDBx:details> </PDBx:em_3d_fitting> </PDBx:em_3d_fittingCategory> Any additional details regarding fitting of atomic coordinates into the 3d-em volume. partial The method used to fit atomic coordinates into the 3dem reconstructed map. The overall B (temperature factor) value for the 3d-em volume. The type of protocol used in the refinement. rigid body A flag to indicate whether fitting was carried out in real or reciprocal refinement space. This data item is a pointer to attribute name in category software in the category. The quality of fit of the atomic coordinates into the 3dem volume map. best visual fit using the program O The value of attribute id in category em_3d_fitting must uniquely identify a fitting procedure of atomic coordinates into 3dem reconstructed volume map. This data item is a pointer to _entry_id in the ENTRY category. Data items in the 3D_FITTING_LIST category lists the methods of fitting atomic coordinates from a PDB file into a 3d-em volume map file Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_3d_fitting_listCategory> <PDBx:em_3d_fitting_list id="1"> <PDBx:pdb_entry_id>1VCQ</PDBx:pdb_entry_id> </PDBx:em_3d_fitting_list> </PDBx:em_3d_fitting_listCategory> The chain id for the entry used in fitting. The PDB code for the entry used in fitting. This data item is a unique identifier. The value of attribute 3d_fitting_id in category em_3d_fitting_list is a pointer to attribute id in category em_3d_fitting in the 3d_fitting category Data items in the EM_3D_RECONSTRUCTION category record details of the 3D reconstruction procedure from 2D projections. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_3d_reconstructionCategory> <PDBx:em_3d_reconstruction entry_id="1DYL" id="1"> <PDBx:method>CROSS-COMMON LINES</PDBx:method> <PDBx:citation_id>1</PDBx:citation_id> <PDBx:resolution>9</PDBx:resolution> <PDBx:nominal_pixel_size>2.64</PDBx:nominal_pixel_size> <PDBx:actual_pixel_size>2.52</PDBx:actual_pixel_size> </PDBx:em_3d_reconstruction> </PDBx:em_3d_reconstructionCategory> The actual pixel size of projection set of images. This data item is a pointer to attribute id in category citation in the CITATION category. The CTF-correction method. The Contrast Transfer Function CTF compensation for low contrast specimens (e.g. frozen-hydrated), for which phase contrast is the only significant mechanism, then higher defocus levels must be used to achieve any significant transfer, and several images at different focus levels must be combined to complete the information lost from the transfer gaps of any one image. The CTF correction can be applied to each extracted particle separately or to the whole micrograph after digitisation. The simplest level of compensation is to reverse phases at the negative lobes of the CTF. CTF correction of each particle Any additional details used in the 3d reconstruction. The magnification calibration method for the 3d reconstruction. The algorithm method used for the 3d-reconstruction. cross-common lines The nominal pixel size of the projection set of images. The final resolution (in angstroms)of the 3d reconstruction. The method used to determine the final resolution of the 3d reconstruction. The Fourier Shell Correlation criterion as a measure of resolution is based on the concept of splitting the (2D) data set into two halves; averaging each and comparing them using the Fourier Ring Correlation (FRC) technique. FSC at 0.5 cut-off This data item is a pointer to attribute id in category entry in the ENTRY category. The value of attribute id in category em_3d_reconstruction must uniquely identify the 3d reconstruction. Data items in the EM_ASSEMBLY category record details about the type of complex assembly that describes the nature of the sample studied. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_assemblyCategory> <PDBx:em_assembly id="1" entry_id="1DYL"> <PDBx:name>virus</PDBx:name> <PDBx:aggregation_state>ICOSAHEDRAL</PDBx:aggregation_state> <PDBx:composition>virus</PDBx:composition> <PDBx:num_components>1</PDBx:num_components> </PDBx:em_assembly> </PDBx:em_assemblyCategory> A description of the aggregation state of the assembly. The known composition of the assembly. A description of any additional details describing the observed sample. This structure was preferentially oriented (end-on)on the grid. The structure was monodisperse. The value (in megadaltons) of the experimentally determined molecular weight of the assembly. The method used in determining the molecular weight. The value (in megadaltons) of the theoretically determined molecular weight of the assembly. The name of the assembly of observed complexes. The number of components of the biological assembly. The value of attribute id in category em_assembly must uniquely identify a collection of observed complexes. This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the BUFFER category record details of the sample buffer. Any additional details to do with buffer. aerated The name of the buffer. Acetic acid The value of attribute id in category em_buffer must uniquely identify the sample buffer. Constituents of buffer in sample Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_buffer_componentsCategory> <PDBx:em_buffer_components buffer_id="1" id="1"> <PDBx:name>NaCl</PDBx:name> <PDBx:volume>0.200 </PDBx:volume> <PDBx:conc>4 </PDBx:conc> </PDBx:em_buffer_components> <PDBx:em_buffer_components buffer_id="1" id="2"> <PDBx:name>Acetic Acid</PDBx:name> <PDBx:volume>0.047 </PDBx:volume> <PDBx:conc>100</PDBx:conc> </PDBx:em_buffer_components> <PDBx:em_buffer_components buffer_id="1" id="3"> <PDBx:name>water</PDBx:name> <PDBx:volume>0.700 </PDBx:volume> <PDBx:conc>neat</PDBx:conc> </PDBx:em_buffer_components> </PDBx:em_buffer_componentsCategory> The millimolar concentration of buffer component. 200 Any additional details to do with buffer composition. pH adjusted with NaOH The name of each buffer component. Acetic acid The volume of buffer component. 0.200 This data item is a pointer to attribute id in category em_buffer in the BUFFER category. The value of attribute id in category em_buffer_components must uniquely identify a component of the buffer. Data items in the EM_DETECTOR category record details of the image detector type. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_detectorCategory> <PDBx:em_detector entry_id="1DYL" id="1"> <PDBx:type>KODAK SO163 FILM</PDBx:type> </PDBx:em_detector> </PDBx:em_detectorCategory> Any additional information about the detection system. The detective_quantum_efficiency (DQE)is defined as the square of the signal-to-noise ratio in the recording device divided by the square of the signal-to-ratio in the electron beam: (SIGNAL/NOISE)2 recording device DQE = ------------------------------- (SIGNAL/NOISE)2 electron beam A DQE value of 1 indicates a perfect recorder. "DQE = 0.25" menas that the signal-to-noise ratio is reduced by half in the recording step. (0.5)**2 DQE = --------- = 0.25. (1.0)**2 0.25 The detector type used for recording images. Usually film or CCD camera. This data item is a pointer to attribute id in category entry in the ENTRY category. The value of attribute id in category em_detector must uniquely identify the detector used for imaging. Data items in the EM_ENTITY_ASSEMBLY category record details about each component of the complex. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_entity_assemblyCategory> <PDBx:em_entity_assembly id="1" assembly_id="1"> <PDBx:type>VIRUS</PDBx:type> </PDBx:em_entity_assembly> </PDBx:em_entity_assemblyCategory> Additional details about the component. The cell from which the component was obtained. CHO HELA 3T3 The cellular location of the component. cytoplasm endoplasmic reticulum plasma membrane A flag to indicate whether the component is engineered. The expression system used to produce the component. eschericia coli saccharomyces cerevisiae The plasmid used in the expression system used to produce the component. pBR322 pMB9 The organelle from which the component was obtained. golgi mitochondrion cytoskeleton The common name of the species of the natural organism from which the component was obtained. The species of the natural organism from which the component was obtained. The strain of the natural organism from which the component was obtained, if relevant. DH5a BMH 71-18 The tissue of the natural organism from which the component was obtained. heart liver eye lens The Gene Ontology (GO) identifier for the component. The GO id is the appropriate identifier used by the Gene Ontology Consortium. Reference: Nature Genetics vol 25:25-29 (2000). GO:0005876 GO:0015630 The InterPro (IPR) identifier for the component. The IPR id is the appropriate identifier used by the Interpro Resource. Reference: Nucleic Acid Research vol 29(1):37-40(2001). 001304 002353 The name of the component of the observed assembly. Alternative name of the component. FADV-1 A description of types of components of the assembly of the biological structure. The value of attribute id in category em_entity_assembly must uniquely identify each of the components of the complex. This data item is a pointer to attribute id in category em_assembly in the ASSEMBLY category. Data items in the EM_ENTITY_ASSEMBLY_LIST category record details of the structural elements in each component. Example 1 - microtubule <PDBx:em_entity_assembly_listCategory> <PDBx:em_entity_assembly_list entity_assembly_id="1" id="1" entity_id="1"> <PDBx:oligomeric_details>DIMER</PDBx:oligomeric_details> <PDBx:number_of_copies>2</PDBx:number_of_copies> </PDBx:em_entity_assembly_list> </PDBx:em_entity_assembly_listCategory> The number of copies of the entity. The oligomeric state of the entity. This data item is a pointer to attribute id in category em_entity_assembly in the ENTITY_ASSEMBLY category. The value of attribute id in category em_entity_assembly_list must uniquely identify the component. A pointer to entity id. Data items in the EM_EULER_ANGLE_DISTRIBUTION category record details of assignment of Euler angles for projection sets of particles. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL The euler-alpha angle assignment. 90 The euler-beta angle assignment. 90 Any additional details of the euler angles distribution and assignment. The euler-gamma angle assignment. 0 The value of attribute id in category em_euler_angle_distribution must uniquely identify the euler angle assignments of the projection set used in the final reconstruction. The value of attribute entry_id in category em_euler_angle_distribution is a pointer to the ENTRY category. Data items in the EM_ICOS_VIRUS_SHELLS category record details of the viral shell number, diameter of each shell and triangulation number. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_icos_virus_shellsCategory> <PDBx:em_icos_virus_shells virus_entity_id="1" id="1"> <PDBx:shell_diameter>400</PDBx:shell_diameter> <PDBx:triangulation_num>4</PDBx:triangulation_num> </PDBx:em_icos_virus_shells> </PDBx:em_icos_virus_shellsCategory> The value of the diameter (in angstroms) for each protein shell of the virus. The triangulation number (T number) is a geometric and abstract concept that does not correspond to the structural components of an individul virus. It refers to the organisation of the geometric figure. The triangulation number, T is given by the following relationship: T= h*2 + hk +k*2, where h and k are positive integers which define the position of the five-fold vertex on the original hexagonal net. 4 The value of attribute virus_entity_id in category em_icos_virus_shells is a pointer to attribute id in category em_virus_entity in the VIRUS_ENTITY category. The value of attribute id in category em_em_icos_virus_shells must uniquely identify the number and diameter of each virus protein shell and its triangulation number. Data items in the EM_IMAGE_SCANS category record details of the image scanning device (microdensitometer) and parameters for digitization of the image. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_image_scansCategory> <PDBx:em_image_scans entry_id="1DYL" id="2"> <PDBx:number_digital_images>48</PDBx:number_digital_images> <PDBx:citation_id>1</PDBx:citation_id> </PDBx:em_image_scans> </PDBx:em_image_scansCategory> This data item is a pointer to attribute id in category citation in the CITATION category. Any additional details about scanning images. The number of images scanned and digitised. The optical density range (OD=-log 10 transmission). To the eye OD=1 appears light grey and OD=3 is opaque. 1.4 The number of bits per pixel. 8 The sampling step size (microns) set on the scanner. The scanner model. This data item is a pointer to attribute id in category entry in the ENTRY category. The value of attribute id in category em_image_scans must uniquely identify the images scanned. Data items in the EM_IMAGING category record details about the parameters used in imaging the sample in the electron microscope. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_imagingCategory> <PDBx:em_imaging entry_id="1DYL" id="1"> <PDBx:sample_support_id>1</PDBx:sample_support_id> <PDBx:microscope_model>FEI/PHILIPS CM200 FEG</PDBx:microscope_model> <PDBx:specimen_holder_type>cryotransfer</PDBx:specimen_holder_type> <PDBx:specimen_holder_model>gatan 626-0300</PDBx:specimen_holder_model> <PDBx:date>1998-15-06</PDBx:date> <PDBx:accelerating_voltage>200</PDBx:accelerating_voltage> <PDBx:illumination_mode>bright field</PDBx:illumination_mode> <PDBx:mode>low dose</PDBx:mode> <PDBx:nominal_cs>2.0</PDBx:nominal_cs> <PDBx:nominal_defocus_min>975</PDBx:nominal_defocus_min> <PDBx:nominal_defocus_max>7600</PDBx:nominal_defocus_max> <PDBx:tilt_angle_min>0</PDBx:tilt_angle_min> <PDBx:tilt_angle_max>0</PDBx:tilt_angle_max> <PDBx:nominal_magnification>50000</PDBx:nominal_magnification> <PDBx:electron_source>FEG</PDBx:electron_source> <PDBx:citation_id>1</PDBx:citation_id> <PDBx:temperature>95</PDBx:temperature> </PDBx:em_imaging> </PDBx:em_imagingCategory> A value of accelerating voltage (in kV) used for imaging. 300 The magnification value obtained for a known standard just prior to, during or just after the imaging experiment. 61200 This data item is a pointer to attribute id in category citation in the CITATION category. Date (YYYY-MM-DD) of imaging experiment. 2001-05-08 Any additional imaging details. weak beam illumination The camera length (in millimeters). The camera length is the product of the objective focal length and the combined magnification of the intermediate and projector lenses when the microscope is operated in the diffraction mode. The value of attribute detector_id in category em_imaging must uniquely identify the type of detector used in the experiment. The electron dose received by the specimen (electrons per square angstrom). 0.9 The source of electrons. The electron gun. The type of energy filter spectrometer apparatus. FEI The energy filter range in electron volts (eV)set by spectrometer. 0 - 15 The mode of illumination. The name of the model of microscope. The mode of imaging. The spherical aberration coefficient (Cs) in millimeters, of the objective lens. 1.4 The maximum defocus value of the objective lens (in nanometres) used to obtain the recorded images. 7600 The minimum defocus value of the objective lens (in nanometres) used to obtain the recorded images. 975 The magnification indicated by the microscope readout. 60000 The specimen temperature maximum (degrees Kelvin) for the duration of imaging. The specimen temperature minimum (degrees Kelvin) for the duration of imaging. This data item is a pointer to attribute id in category em_sample_support in the EM_SAMPLE_SUPPORT category. The value of attribute scans_id in category em_imaging must uniquely identify the image_scans used in the experiment. The name of the model of specimen holder used during imaging. The type of specimen holder used during imaging. cryo The mean specimen stage temperature (degrees Kelvin) during imaging in the microscope. The maximum angle at which the specimen was tilted to obtain recorded images. 60 The minimum angle at which the specimen was tilted to obtain recorded images. 0 This data item is a pointer to attribute id in category entry in the ENTRY category. The value of attribute id in category em_imaging must uniquely identify each imaging experiment. Data items in the EM_SAMPLE_PREPARATION category record details of sample conditions prior to loading onto grid support. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_sample_preparationCategory> <PDBx:em_sample_preparation entry_id="1DYL" id="1"> <PDBx:ph>7.6</PDBx:ph> <PDBx:buffer_id>1</PDBx:buffer_id> <PDBx:sample_concentration>5</PDBx:sample_concentration> </PDBx:em_sample_preparation> </PDBx:em_sample_preparationCategory> This data item is a pointer to attribute id in category em_2d_crystal_grow in the 2D_CRYSTAL_GROW category. This data item is a pointer to attribute id in category em_buffer in the BUFFER category. The pH value of the observed sample buffer. The value of the concentration (mg/mL for mg per milliliter) of the complex in the sample. This data item is a pointer to attribute id in category em_sample_support in the EM_SAMPLE_SUPPORT category. The value of attribute id in category em_sample_preparation must uniquely identify the sample preparation. This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the EM_SAMPLE_SUPPORT category record details of the electron microscope grid type, grid support film and pretreatment of whole before sample is applied Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_sample_supportCategory> <PDBx:em_sample_support id="1"> <PDBx:film_material>HOLEY CARBON</PDBx:film_material> <PDBx:grid_material>COPPER</PDBx:grid_material> <PDBx:grid_mesh_size>400</PDBx:grid_mesh_size> <PDBx:grid_type>MESH</PDBx:grid_type> <PDBx:pretreatment>GLOW DISCHARGE</PDBx:pretreatment> <PDBx:citation_id>2</PDBx:citation_id> </PDBx:em_sample_support> </PDBx:em_sample_supportCategory> This data item is a pointer to attribute id in category citation in the CITATION category. A description of any additional details concerning the sample support. This grid plus sample was kept at -170 deg C for a month before use The support material covering the em grid. The name of the material from which the grid is made. The value of the mesh size (per inch) of the em grid. 400 A description of the grid type. A description of the method used to produce the support film. 1%formvar in chloroform cast on distilled water A description of the grid plus support film pretreatment. glow-discharged for 30 sec in argon The value of attribute id in category em_sample_support must uniquely identify the sample support. Data items in the EM_VIRUS_ENTITY category record details of the icosahedral virus. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_virus_entityCategory> <PDBx:em_virus_entity id="1" entity_assembly_id="1"> <PDBx:virus_host_category>VERTERBRATES</PDBx:virus_host_category> <PDBx:virus_host_species>HOMO SAPIENS</PDBx:virus_host_species> <PDBx:virus_type>VIRUS</PDBx:virus_type> <PDBx:virus_isolate>STRAIN</PDBx:virus_isolate> <PDBx:ictvdb_id>00.073.0.01.023</PDBx:ictvdb_id> <PDBx:enveloped>YES</PDBx:enveloped> <PDBx:empty>NO</PDBx:empty> </PDBx:em_virus_entity> </PDBx:em_virus_entityCategory> Flag to indicate if the virus is empty or not. Flag to indicate if the virus is enveloped or not. The International Committee on Taxonomy of Viruses (ICTV) Taxon Identifier is the Virus Code used throughout the ICTV database (ICTVdb). The ICTVdb id is the appropriate identifier used by the International Committee on Taxonomy of Viruses Resource. Reference: Virus Taxonomy, Academic Press (1999). ISBN:0123702003. 01.0.2.0.001 01.0.2.0.002 The host category description for the virus. The host cell from which the virus was isolated. HELA CHO The host species from which the virus was isolated. homo sapiens gallus gallus The isolate from which the virus was obtained. The type of virus. Is the unique identifier for VIRUS_ENTITY category. This data item is a pointer to attribute id in category em_virus_entity in the ENTITY_ASSEMBLY category. Data items in the EM_VITRIFICATION category record details about the method and cryogen used in rapid freezing of the sample on the grid prior to its insertion in the electron microscope Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_vitrificationCategory> <PDBx:em_vitrification entry_id="1DYL" id="1"> <PDBx:sample_preparation_id>1</PDBx:sample_preparation_id> <PDBx:cryogen_name>ETHANE</PDBx:cryogen_name> <PDBx:humidity>90</PDBx:humidity> <PDBx:temp>95</PDBx:temp> <PDBx:method>PLUNGE VITRIFICATION</PDBx:method> <PDBx:citation_id>1</PDBx:citation_id> <PDBx:details> SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626-0300 CRYOTRANSFER HOLDER. </PDBx:details> </PDBx:em_vitrification> </PDBx:em_vitrificationCategory> This data item is a pointer to attribute id in category citation in the CITATION category. This is the name of the cryogen. Any additional details relating to vitrification. argon atmosphere The humidity (%) in the vicinity of the vitrification process. 90 The type of instrument used in the vitrification process. Reichert plunger The procedure for vitrification. blot for 2 seconds before plunging This data item is a pointer to attribute id in category em_sample_preparation in the EM_SAMPLE_PREPARATION category. The temperature (in degrees Kelvin) at which vitrification took place. 4.2 The length of time after an event effecting the sample that vitrification was induced and a description of the event. 30 msec after spraying with effector' The value of attribute id in category em_vitrification must uniquely identify the vitrification procedure. This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the ENTITY category record details (such as chemical composition, name, and source) about the molecular entities that are present in the crystallographic structure. Items in the various ENTITY sub-categories provide a full chemical description of these molecular entities. Entities are of three types: polymer, non-polymer and water. Note that the water category includes only water; ordered solvent such as sulfate ion or acetone would be described as individual non-polymer entities. The ENTITY category is specific to macromolecular CIF applications, and replaces the function of the CHEMICAL category in the CIF core. It is important to remember that the ENTITY data are not the result of the crystallographic experiment; those results are represented in the ATOM_SITE data items. ENTITY data items describe the chemistry of the molecules under investigation, and can most usefully be thought of as the ideal groups to which the structure is restrained or constrained during refinement. It is also important to remember that entities do not correspond directly to the enumeration of the contents of the asymmetric unit. Entities are described only once, even in those structures that contain multiple observations of an entity. The STRUCT_ASYM data items, which reference the entity list, describe and label the contents of the asymmetric unit. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:entityCategory> <PDBx:entity id="1"> <PDBx:type>polymer</PDBx:type> <PDBx:formula_weight>10916</PDBx:formula_weight> <PDBx:details> The enzymatically competent form of HIV protease is a dimer. This entity corresponds to one monomer of an active dimer.</PDBx:details> </PDBx:entity> <PDBx:entity id="2"> <PDBx:type>non-polymer</PDBx:type> <PDBx:formula_weight>762</PDBx:formula_weight> </PDBx:entity> <PDBx:entity id="3"> <PDBx:type>water</PDBx:type> <PDBx:formula_weight>18</PDBx:formula_weight> </PDBx:entity> </PDBx:entityCategory> A description of special aspects of the entity. Formula mass in daltons of the entity. A description of the entity, with the name of the entity in parenthesis. Maps to PDB compound name. DNA (5'-D(*GP*(CH3)CP*GP*(CH3)CP*GP*C)-3') PROFLAVINE PROTEIN (DEOXYRIBONUCLEASE I (E.C.3.1.21.1)) Enzyme Commission (EC) number(s) 2.7.7.7 Experimentally determined formula mass in daltons of the entity Method used to determine attribute pdbx_formula_weight_exptl in category entity. MASS SPEC Entity fragment description(s). KLENOW FRAGMENT REPLICASE OPERATOR HAIRPIN C-TERMINAL DOMAIN Description(s) of any chemical or post-translational modifications Details about any entity mutation(s). Y31H DEL(298-323) A place holder for the number of molecules of the entity in the entry. 1.0 2.0 3.0 An identifier for the parent entity if this entity is part of a complex entity. For instance a chimeric entity may be decomposed into several independent chemical entities where each component entity was obtained from a different source. 1 2 3 The method by which the sample for the entity was produced. Entities isolated directly from natural sources (tissues, soil samples, etc.) are expected to have further information in the ENTITY_SRC_NAT category. Entities isolated from genetically manipulated sources are expected to have further information in the ENTITY_SRC_GEN category. The value of attribute target_id in category entity points to a target idenitifier from which this entity was generated. Defines the type of the entity. Polymer entities are expected to have corresponding ENTITY_POLY and associated entries. Non-polymer entities are expected to have corresponding CHEM_COMP and associated entries. Water entities are not expected to have corresponding entries in the ENTITY category. The value of attribute id in category entity must uniquely identify a record in the ENTITY list. Note that this item need not be a number; it can be any unique identifier. Data items in the ENTITY_KEYWORDS category specify keywords relevant to the molecular entities. Note that this list of keywords is separate from the list that is used for the STRUCT_BIOL data items, and is intended to provide only the information that one would know about the molecular entity *if one did not know its structure*. Hence polypeptides are simply polypeptides, and not cytokines or beta-alpha-barrels, and polyribonucleic acids are simply poly-RNA, and not transfer- RNA. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:entity_keywordsCategory> <PDBx:entity_keywords entity_id="1"> <PDBx:text>polypeptide</PDBx:text> </PDBx:entity_keywords> <PDBx:entity_keywords entity_id="2"> <PDBx:text>natural product</PDBx:text> </PDBx:entity_keywords> <PDBx:entity_keywords entity_id="2"> <PDBx:text>inhibitor</PDBx:text> </PDBx:entity_keywords> <PDBx:entity_keywords entity_id="2"> <PDBx:text>reduced peptide</PDBx:text> </PDBx:entity_keywords> </PDBx:entity_keywordsCategory> Enzyme Commission (EC) number(s) 2.7.7.7 Entity fragment description(s). KLENOW FRAGMENT REPLICASE OPERATOR HAIRPIN C-TERMINAL DOMAIN Entity mutation description(s). Y31H DEL(298-323) Keywords describing this entity. polypeptide natural product polysaccharide This data item is a pointer to attribute id in category entity in the ENTITY category. Data items in the ENTITY_LINK category give details about the linkages between entities. Example 1 - based on A description of special aspects of a linkage between chemical components in the structure. The entity id of the first of the two entities joined by the linkage. This data item is a pointer to attribute id in category entity in the ENTITY category. The entity id of the second of the two entities joined by the linkage. This data item is a pointer to attribute id in category entity in the ENTITY category. For a polymer entity, the sequence number in the first of the two entities containing the linkage. This data item is a pointer to attribute num in category entity_poly_seq in the ENTITY_POLY_SEQ category. For a polymer entity, the sequence number in the second of the two entities containing the linkage. This data item is a pointer to attribute num in category entity_poly_seq in the ENTITY_POLY_SEQ category. This data item is a pointer to attribute id in category chem_link in the CHEM_LINK category. Data items in the ENTITY_NAME_COM category record the common name or names associated with the entity. In some cases, the entity name may not be the same as the name of the biological structure. For instance, hemoglobin alpha chain would be the entity common name, not hemoglobin. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:entity_name_comCategory> <PDBx:entity_name_com entity_id="1" name="HIV-1 protease monomer"></PDBx:entity_name_com> <PDBx:entity_name_com entity_id="1" name="HIV-1 PR monomer"></PDBx:entity_name_com> <PDBx:entity_name_com entity_id="2" name="acetyl-pepstatin"></PDBx:entity_name_com> <PDBx:entity_name_com entity_id="2" name="acetyl-Ile-Val-Asp-Statine-Ala-Ile-Statine"></PDBx:entity_name_com> <PDBx:entity_name_com entity_id="3" name="water"></PDBx:entity_name_com> </PDBx:entity_name_comCategory> This data item is a pointer to attribute id in category entity in the ENTITY category. A common name for the entity. HIV protease monomer hemoglobin alpha chain 2-fluoro-1,4-dichloro benzene Data items in the ENTITY_NAME_SYS category record the systematic name or names associated with the entity, and tell which system was is the source of the systematic name. In some cases, the entity name may not be the same as the name of the biological structure. For instance, hemoglobin alpha chain would be the entity common name, not hemoglobin. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:entity_name_sysCategory> <PDBx:entity_name_sys entity_id="1" name="ECx.x.x.x"></PDBx:entity_name_sys> <PDBx:entity_name_sys entity_id="2" name="acetyl-Ile-Val-Asp-Sta-Ala-Ile-Sta"></PDBx:entity_name_sys> <PDBx:entity_name_sys entity_id="3" name="H(2)0"></PDBx:entity_name_sys> </PDBx:entity_name_sysCategory> The system used to generate the systematic name of the entity. chemical abstracts conventions enzyme convention Sigma catalog This data item is a pointer to attribute id in category entity in the ENTITY category. The systematic name for the entity. x,x,pyranoside EC 2.1.1.1 2-fluoro-1,4-dichloro benzene Data items in the ENTITY_POLY category record details about the polymer, such as the type of the polymer, the number of monomers, and whether it has non-standard features. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:entity_polyCategory> <PDBx:entity_poly entity_id="1"> <PDBx:type>polypeptide(L)</PDBx:type> <PDBx:nstd_chirality>no</PDBx:nstd_chirality> <PDBx:nstd_linkage>no</PDBx:nstd_linkage> <PDBx:nstd_monomer>no</PDBx:nstd_monomer> </PDBx:entity_poly> </PDBx:entity_polyCategory> A flag to indicate whether or not the polymer contains at least one monomer unit with chirality different from that specified in attribute type in category entity_poly. A flag to indicate whether or not the polymer contains at least one monomer-to-monomer linkage different from that implied by attribute type in category entity_poly. A flag to indicate whether or not the polymer contains at least one monomer that is not considered standard. The number of monomers in the polymer. Chemical sequence expressed as string of one-letter amino acid codes. Modifications and non-standard amino acids are coded as X. A for alanine or adenine B for ambiguous asparagine/aspartic-acid R for arginine N for asparagine D for aspartic-acid C for cysteine or cystine or cytosine Q for glutamine E for glutamic-acid Z for ambiguous glutamine/glutamic acid G for glycine or guanine H for histidine I for isoleucine L for leucine K for lysine M for methionine F for phenylalanine P for proline S for serine T for threonine or thymine W for tryptophan Y for tyrosine V for valine U for uracil O for water X for other Cannonical chemical sequence expressed as string of one-letter amino acid codes. Modifications are coded as the parent amino acid where possible. A for alanine or adenine B for ambiguous asparagine/aspartic-acid R for arginine N for asparagine D for aspartic-acid C for cysteine or cystine or cytosine Q for glutamine E for glutamic-acid Z for ambiguous glutamine/glutamic acid G for glycine or guanine H for histidine I for isoleucine L for leucine K for lysine M for methionine F for phenylalanine P for proline S for serine T for threonine or thymine W for tryptophan Y for tyrosine V for valine U for uracil MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGAAFNVEFD The PDB strand/chain id(s) corresponding to this polymer entity. A B A,B,C The type of the polymer. A description of special aspects of the polymer type. monomer Ala 16 is a D-amino acid the oligomer contains alternating RNA and DNA units This data item is a pointer to attribute id in category entity in the ENTITY category. Data items in the ENTITY_POLY_SEQ category specify the sequence of monomers in a polymer. Allowance is made for the possibility of microheterogeneity in a sample by allowing a given sequence number to be correlated with more than one monomer id - the corresponding ATOM_SITE entries should reflect this heterogeneity. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:entity_poly_seqCategory> <PDBx:entity_poly_seq entity_id="1" num="1" mon_id="PRO"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" num="2" mon_id="GLN"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" num="3" mon_id="ILE"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" num="4" mon_id="THR"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" num="5" mon_id="LEU"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" num="6" mon_id="TRP"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" num="7" mon_id="GLN"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" num="8" mon_id="ARG"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" num="9" mon_id="PRO"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" num="10" mon_id="LEU"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" num="11" mon_id="VAL"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" num="12" mon_id="THR"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" num="13" mon_id="ILE"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" num="14" mon_id="LYS"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" num="15" mon_id="ILE"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" num="16" mon_id="GLY"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" num="17" mon_id="GLY"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" num="18" mon_id="GLN"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" num="19" mon_id="LEU"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" num="20" mon_id="LYS"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" num="21" mon_id="GLU"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" num="22" mon_id="ALA"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" num="23" mon_id="LEU"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" num="24" mon_id="LEU"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" num="25" mon_id="ASP"></PDBx:entity_poly_seq> </PDBx:entity_poly_seqCategory> A flag to indicate whether or not this monomer in the polymer is heterogeneous in sequence. This would be a rare phenomenon. This data item is a pointer to attribute id in category entity in the ENTITY category. The value of attribute num in category entity_poly_seq must uniquely and sequentially identify a record in the ENTITY_POLY_SEQ list. Note that this item must be a number, and that the sequence numbers must progress in increasing numerical order. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. Data items in the ENTITY_SRC_GEN category record details of the source from which the entity was obtained, in those cases where the source was a genetically manipulated one. The following are treated separately: Items pertaining to the tissue from which the gene was obtained, items pertaining to the host organism for gene expression and items pertaining to the actual producing organism (plasmid). Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:entity_src_genCategory> <PDBx:entity_src_gen entity_id="1"> <PDBx:gene_src_common_name>HIV-1</PDBx:gene_src_common_name> <PDBx:gene_src_strain>NY-5</PDBx:gene_src_strain> <PDBx:host_org_common_name>bacteria</PDBx:host_org_common_name> <PDBx:host_org_genus>Escherichia</PDBx:host_org_genus> <PDBx:host_org_species>coli</PDBx:host_org_species> <PDBx:plasmid_name>pB322</PDBx:plasmid_name> </PDBx:entity_src_gen> </PDBx:entity_src_genCategory> A unique identifier for the expression system. This should be extracted from a local list of expression systems. The common name of the natural organism from which the gene was obtained. man yeast bacteria A description of special aspects of the natural organism from which the gene was obtained. A string to indicate the life-cycle or cell development cycle in which the gene is expressed and the mature protein is active. The genus of the natural organism from which the gene was obtained. Homo Saccharomyces Escherichia The species of the natural organism from which the gene was obtained. sapiens cerevisiae coli The strain of the natural organism from which the gene was obtained, if relevant. DH5a BMH 71-18 The tissue of the natural organism from which the gene was obtained. heart liver eye lens The sub-cellular fraction of the tissue of the natural organism from which the gene was obtained. mitochondria nucleus membrane The common name of the organism that served as host for the production of the entity. yeast bacteria A description of special aspects of the organism that served as host for the production of the entity. The genus of the organism that served as host for the production of the entity. Saccharomyces Escherichia The species of the organism that served as host for the production of the entity. cerevisiae coli The strain of the organism that served as host for the production of the entity. DH5a BMH 71-18 Information on the source which is not given elsewhere. American Type Culture Collection tissue culture number. 6051 Cell type. ENDOTHELIAL The specific line of cells. HELA CELLS Identifies the location inside (or outside) the cell. CYTOPLASM NUCLEUS A domain or fragment of the molecule. CYTOPLASM NUCLEUS Identifies the gene. Organized group of tissues that carries on a specialized function. KIDNEY LIVER PANCREAS Organized structure within cell. MITOCHONDRIA The source plasmid. The source plasmid. Scientific name of the organism. ESCHERICHIA COLI HOMO SAPIENS SACCHAROMYCES CEREVISIAE Identifies the variant. DELTAH1DELTATRP Americal Tissue Culture Collection of the expression system. Specific cell type which expressed the molecule. ENDOTHELIAL A specific line of cells used as the expression system. HELA Identifies the location inside (or outside) the cell which expressed the molecule. CYTOPLASM NUCLEUS Culture collection of the expression system. Specific gene which expressed the molecule. HIV-1 POL GLNS7 U1A (2-98, Y31H, Q36R) Specific organ which expressed the molecule. KIDNEY Specific organelle which expressed the molecule. MITOCHONDRIA The scientific name of the organism that served as host for the production of the entity. ESCHERICHIA COLI HOMO SAPIENS SACCHAROMYCES CEREVISIAE ESCHERICHIA COLI SACCHAROMYCES CEREVISIAE The strain of the organism in which the entity was expressed. AR120 The specific tissue which expressed the molecule. heart liver eye lens The fraction of the tissue which expressed the molecule. mitochondria nucleus membrane Variant of the organism used as the expression system. TRP-LAC LAMBDA DE3 Identifies the vector used. PBIT36 PET15B PUC18 Identifies the type of vector used (plasmid, virus, or cosmid). COSMID PLASMID A description of special aspects of the plasmid that produced the entity in the host organism. The name of the plasmid that produced the entity in the host organism. pET3C pT123sab A pointer to attribute id in category pdbx_construct in the PDBX_CONSTRUCT category. The indentified sequence is the initial construct. This data item is a pointer to attribute id in category entity in the ENTITY category. Data items in the ENTITY_SRC_NAT category record details of the source from which the entity was obtained, in those cases where the entity was isolated directly from a natural tissue. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:entity_src_natCategory> <PDBx:entity_src_nat entity_id="2"> <PDBx:common_name>bacteria</PDBx:common_name> <PDBx:genus>Actinomycetes</PDBx:genus> <PDBx:species xsi:nil="true" /> <PDBx:details> Acetyl-pepstatin was isolated by Dr. K. Oda, Osaka Prefecture University, and provided to us by Dr. Ben Dunn, University of Florida, and Dr. J. Kay, University of Wales.</PDBx:details> </PDBx:entity_src_nat> </PDBx:entity_src_natCategory> The genus of the organism from which the entity was isolated. man yeast bacteria A description of special aspects of the organism from which the entity was isolated. The genus of the organism from which the entity was isolated. Homo Saccharomyces Escherichia Americal Tissue Culture Collection number. 6051 A particular cell type. BHK-21 The specific line of cells. HELA Identifies the location inside (or outside) the cell. A domain or fragment of the molecule. Organized group of tissues that carries on a specialized function. KIDNEY Organized structure within cell. MITOCHONDRIA Scientific name of the organism of the natural source. BOS TAURUS SUS SCROFA ASPERGILLUS ORYZAE Details about the plasmid. PLC28 DERIVATIVE The plasmid containing the gene. pB322 Identifies the secretion from which the molecule was isolated. saliva urine venom Identifies the variant. The species of the organism from which the entity was isolated. sapiens cerevisiae coli The strain of the organism from which the entity was isolated. DH5a BMH 71-18 The tissue of the organism from which the entity was isolated. heart liver eye lens The sub-cellular fraction of the tissue of the organism from which the entity was isolated. mitochondria nucleus membrane This data item is a pointer to attribute id in category entity in the ENTITY category. There is only one item in the ENTRY category, attribute id in category entry. This data item gives a name to this entry, and is indirectly a key to the categories (such as CELL, GEOM, EXPTL) that describe information pertinent to the entire data block. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:entryCategory> <PDBx:entry id="5HVP"></PDBx:entry> </PDBx:entryCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. <PDBx:entryCategory> <PDBx:entry id="TOZ"></PDBx:entry> </PDBx:entryCategory> The value of attribute id in category entry identifies the data block. Note that this item need not be a number; it can be any unique identifier. Data items in the ENTRY_LINK category record the relationships between the current data block identified by attribute id in category entry and other data blocks within the current file which may be referenced in the current data block. Example 1 - example file for the one-dimensional incommensurately modulated structure of K~2~SeO~4~. <PDBx:entry_linkCategory> <PDBx:entry_link id="KSE_COM" entry_id="KSE_TEXT"> <PDBx:details>experimental data common to ref./mod. structures</PDBx:details> </PDBx:entry_link> <PDBx:entry_link id="KSE_REF" entry_id="KSE_TEXT"> <PDBx:details>reference structure</PDBx:details> </PDBx:entry_link> <PDBx:entry_link id="KSE_MOD" entry_id="KSE_TEXT"> <PDBx:details>modulated structure</PDBx:details> </PDBx:entry_link> </PDBx:entry_linkCategory> The description of the relationship between the data blocks identified _entry_link.id and _entry_link.entry_id. The value of attribute id in category entry_link identifies a data block related to the data block identified by attribute id in category entry_link. This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the EXPTL category record details about the growth of the crystal, and about experimental measurements on the crystal, such as shape, size, density, and so on. Example 1 - based on laboratory records for Yb(S-C5H4N)2 (THF)4 <PDBx:exptlCategory> <PDBx:exptl entry_id="datablock1"> <PDBx:absorpt_coefficient_mu>1.22</PDBx:absorpt_coefficient_mu> <PDBx:absorpt_correction_T_max>0.896</PDBx:absorpt_correction_T_max> <PDBx:absorpt_correction_T_min>0.802</PDBx:absorpt_correction_T_min> <PDBx:absorpt_correction_type>integration</PDBx:absorpt_correction_type> <PDBx:absorpt_process_details> Gaussian grid method from SHELX76 Sheldrick, G. M., &quot;SHELX-76: structure determination and refinement program&quot;, Cambridge University, UK, 1976</PDBx:absorpt_process_details> <PDBx:crystals_number>1</PDBx:crystals_number> <PDBx:details> Enraf-Nonius LT2 liquid nitrogen variable-temperature device used</PDBx:details> <PDBx:method>single-crystal x-ray diffraction</PDBx:method> <PDBx:method_details> graphite monochromatized Cu K(alpha) fixed tube and Enraf-Nonius CAD4 diffractometer used</PDBx:method_details> </PDBx:exptl> </PDBx:exptlCategory> The absorption coefficient mu in reciprocal millimetres calculated from the atomic content of the cell, the density and the radiation wavelength. The maximum transmission factors for the crystal and radiation. These factors are also referred to as the absorption correction A or 1/A*. The minimum transmission factors for the crystal and radiation. These factors are also referred to as the absorption correction A or 1/A*. The absorption correction type and method. The value 'empirical' should NOT be used unless no more detailed information is available. Description of the absorption process applied to the intensities. A literature reference should be supplied for psi-scan techniques. Tompa analytical The total number of crystals used in the measurement of intensities. Any special information about the experimental work prior to the intensity measurement. See also attribute preparation in category exptl_crystal. The method used in the experiment. single-crystal x-ray diffraction single-crystal neutron diffraction single-crystal electron diffraction fiber x-ray_diffraction fiber neutron_diffraction fiber electron_diffraction single-crystal joint x-ray and neutron diffraction single-crystal joint x-ray and electron diffraction solution_ mr solid-state nmr theoretical model other A description of special aspects of the experimental method. 29 structures minimized average structure This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the EXPTL_CRYSTAL category record details about experimental measurements on the crystal or crystals used, such as shape, size, density, and so on. Example 1 - based on laboratory records for Yb(S-C5H4N)2 (THF)4 <PDBx:exptl_crystalCategory> <PDBx:exptl_crystal id="xst2l"> <PDBx:colour>pale yellow</PDBx:colour> <PDBx:density_diffrn>1.113</PDBx:density_diffrn> <PDBx:density_Matthews>1.01</PDBx:density_Matthews> <PDBx:density_meas>1.11</PDBx:density_meas> <PDBx:density_meas_temp>294.5</PDBx:density_meas_temp> <PDBx:density_method>neutral buoyancy</PDBx:density_method> <PDBx:density_percent_sol>0.15</PDBx:density_percent_sol> <PDBx:description>hexagonal rod, uncut</PDBx:description> <PDBx:F_000>202</PDBx:F_000> <PDBx:preparation> hanging drop, crystal soaked in 10&#37; ethylene glycol for 10 h, then placed in nylon loop at data collection time</PDBx:preparation> <PDBx:size_max>0.30</PDBx:size_max> <PDBx:size_mid>0.20</PDBx:size_mid> <PDBx:size_min>0.05</PDBx:size_min> <PDBx:size_rad>0.025</PDBx:size_rad> </PDBx:exptl_crystal> </PDBx:exptl_crystalCategory> The effective number of electrons in the crystal unit cell contributing to F(000). It may contain dispersion contributions, and is calculated as F(000) = [ sum (f~r~^2^ + f~i~^2^) ]^1/2^ f~r~ = real part of the scattering factors at theta = 0 f~i~ = imaginary part of the scattering factors at theta = 0 The colour of the crystal. dark green The density of the crystal, expressed as the ratio of the volume of the asymmetric unit to the molecular mass of a monomer of the structure, in units of angstroms^3^ per dalton. Ref: Matthews, B. W. (1960). J. Mol. Biol., 33, 491-497 Density values calculated from crystal cell and contents. The units are megagrams per cubic metre (grams per cubic centimetre). Density values measured using standard chemical and physical methods. The units are megagrams per cubic metre (grams per cubic centimetre). The temperature in kelvins at which attribute density_meas in category exptl_crystal was determined. The method used to measure attribute density_meas in category exptl_crystal. Density value P calculated from crystal cell and contents, expressed as percent solvent. P = 1 - (1.23 N MMass) / V N = the number of molecules in the unit cell MMass = the molecular mass of each molecule (gm/mole) V = the volume of the unit cell (A^3^) 1.23 = the evaluated conversion factor: (0.74 cm^3^/gm^3^) (10^24^ A^3^/cm^3^) -------------------------------------- (6.02*10^23^) moles/molecule where 0.74 is an assumed value for the partial specific volume of the molecule A description of the quality and habit of the crystal. Dimensional data are better placed in the data items in the EXPTL_CRYSTAL_FACE category. The image format for the file containing the image of crystal specified as an RFC2045/RFC2046 mime type. jpeg gif tiff The URL for an a file containing the image of crystal. Details of crystal growth and preparation of the crystal (e.g. mounting) prior to the intensity measurements. mounted in an argon-filled quartz capillary The maximum dimension of the crystal. This item may appear in a list with attribute id in category exptl_crystal if multiple crystals are used in the experiment. The medial dimension of the crystal. This item may appear in a list with attribute id in category exptl_crystal if multiple crystals are used in the experiment. The minimum dimension of the crystal. This item may appear in a list with attribute id in category exptl_crystal if multiple crystals are used in the experiment. The radius of the crystal, if the crystal is a sphere or a cylinder. This item may appear in a list with attribute id in category exptl_crystal if multiple crystals are used in the experiment. The value of attribute id in category exptl_crystal must uniquely identify a record in the EXPTL_CRYSTAL list. Note that this item need not be a number; it can be any unique identifier. Data items in the EXPTL_CRYSTAL_FACE category record details of the crystal faces. Example 1 - based on laboratory records for Yb(S-C5H4N)2 (THF)4 for the 100 face of crystal, xstl1. <PDBx:exptl_crystal_faceCategory> <PDBx:exptl_crystal_face crystal_id="xstl1" index_h="1" index_k="0" index_l="0"> <PDBx:diffr_chi>42.56</PDBx:diffr_chi> <PDBx:diffr_kappa>30.23</PDBx:diffr_kappa> <PDBx:diffr_phi>-125.56</PDBx:diffr_phi> <PDBx:diffr_psi>-0.34</PDBx:diffr_psi> <PDBx:perp_dist>0.025</PDBx:perp_dist> </PDBx:exptl_crystal_face> </PDBx:exptl_crystal_faceCategory> The chi diffractometer setting angle in degrees for a specific crystal face associated with attribute perp_dist in category exptl_crystal_face. The kappa diffractometer setting angle in degrees for a specific crystal face associated with attribute perp_dist in category exptl_crystal_face. The phi diffractometer setting angle in degrees for a specific crystal face associated with attribute perp_dist in category exptl_crystal_face. The psi diffractometer setting angle in degrees for a specific crystal face associated with attribute perp_dist in category exptl_crystal_face. The perpendicular distance in millimetres of the face to the centre of rotation of the crystal. This data item is a pointer to attribute id in category exptl_crystal in the EXPTL_CRYSTAL category. Miller index h of the crystal face associated with the value attribute perp_dist in category exptl_crystal_face. Miller index k of the crystal face associated with the value attribute perp_dist in category exptl_crystal_face. Miller index l of the crystal face associated with the value attribute perp_dist in category exptl_crystal_face. Data items in the EXPTL_CRYSTAL_GROW category record details about the conditions and methods used to grow the crystal. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:exptl_crystal_growCategory> <PDBx:exptl_crystal_grow crystal_id="1"> <PDBx:method>hanging drop</PDBx:method> <PDBx:apparatus>Linbro plates</PDBx:apparatus> <PDBx:atmosphere>room air</PDBx:atmosphere> <PDBx:pH>4.7</PDBx:pH> <PDBx:temp>18(3)</PDBx:temp> <PDBx:time>approximately 2 days</PDBx:time> </PDBx:exptl_crystal_grow> </PDBx:exptl_crystal_growCategory> The physical apparatus in which the crystal was grown. Linbro plate sandwich box ACA plates The nature of the gas or gas mixture in which the crystal was grown. room air nitrogen argon A description of special aspects of the crystal growth. Solution 2 was prepared as a well solution and mixed. A droplet containing 2 \ml of solution 1 was delivered onto a cover slip; 2 \ml of solution 2 was added to the droplet without mixing. Crystal plates were originally stored at room temperature for 1 week but no nucleation occurred. They were then transferred to 4 degrees C, at which temperature well formed single crystals grew in 2 days. The dependence on pH for successful crystal growth is very sharp. At pH 7.4 only showers of tiny crystals grew, at pH 7.5 well formed single crystals grew, at pH 7.6 no crystallization occurred at all. The method used to grow the crystals. batch precipitation batch dialysis hanging drop vapor diffusion sitting drop vapor diffusion A literature reference that describes the method used to grow the crystals. McPherson et al., 1988 The pH at which the crystal was grown. If more than one pH was employed during the crystallization process, the final pH should be noted here and the protocol involving multiple pH values should be described in attribute details in category exptl_crystal_grow. 7.4 7.6 4.3 Text description of crystal grow procedure. PEG 4000, potassium phosphate, magnesium chloride, cacodylate The range of pH values at which the crystal was grown. Used when a point estimate of pH is not appropriate. 5.6 - 6.4 The ambient pressure in kilopascals at which the crystal was grown. The estimated standard deviation of attribute pressure in category exptl_crystal_grow. A description of the protocol used for seeding the crystal growth. macroseeding Microcrystals were introduced from a previous crystal growth experiment by transfer with a human hair. A literature reference that describes the protocol used to seed the crystal. Stura et al., 1989 The temperature in kelvins at which the crystal was grown. If more than one temperature was employed during the crystallization process, the final temperature should be noted here and the protocol involving multiple temperatures should be described in attribute details in category exptl_crystal_grow. A description of special aspects of temperature control during crystal growth. The estimated standard deviation of attribute temp in category exptl_crystal_grow. The approximate time that the crystal took to grow to the size used for data collection. overnight 2-4 days 6 months This data item is a pointer to attribute id in category exptl_crystal in the EXPTL_CRYSTAL category. Data items in the EXPTL_CRYSTAL_GROW_COMP category record details about the components of the solutions that were 'mixed' (by whatever means) to produce the crystal. In general, solution 1 is the solution that contains the molecule to be crystallized and solution 2 is the solution that contains the precipitant. However, the number of solutions required to describe the crystallization protocol is not limited to 2. Details of the crystallization protocol should be described in EXPTL_CRYSTAL_GROW_DETAILS, using the solutions described in EXPTL_CRYSTAL_GROW_COMP. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:exptl_crystal_grow_compCategory> <PDBx:exptl_crystal_grow_comp crystal_id="1" id="1"> <PDBx:sol_id>1</PDBx:sol_id> <PDBx:name>HIV-1 protease</PDBx:name> <PDBx:volume>0.002 ml</PDBx:volume> <PDBx:conc>6 mg/ml</PDBx:conc> <PDBx:details> The protein solution was in a buffer containing 25 mM NaCl, 100 mM NaMES/ MES buffer, pH 7.5, 3 mM NaAzide</PDBx:details> </PDBx:exptl_crystal_grow_comp> <PDBx:exptl_crystal_grow_comp crystal_id="1" id="2"> <PDBx:sol_id>2</PDBx:sol_id> <PDBx:name>NaCl</PDBx:name> <PDBx:volume>0.200 ml</PDBx:volume> <PDBx:conc>4 M</PDBx:conc> <PDBx:details>in 3 mM NaAzide</PDBx:details> </PDBx:exptl_crystal_grow_comp> <PDBx:exptl_crystal_grow_comp crystal_id="1" id="3"> <PDBx:sol_id>2</PDBx:sol_id> <PDBx:name>Acetic Acid</PDBx:name> <PDBx:volume>0.047 ml</PDBx:volume> <PDBx:conc>100 mM</PDBx:conc> <PDBx:details>in 3 mM NaAzide</PDBx:details> </PDBx:exptl_crystal_grow_comp> <PDBx:exptl_crystal_grow_comp crystal_id="1" id="4"> <PDBx:sol_id>2</PDBx:sol_id> <PDBx:name>Na Acetate</PDBx:name> <PDBx:volume>0.053 ml</PDBx:volume> <PDBx:conc>100 mM</PDBx:conc> <PDBx:details> in 3 mM NaAzide. Buffer components were mixed to produce a pH of 4.7 according to a ratio calculated from the pKa. The actual pH of solution 2 was not measured.</PDBx:details> </PDBx:exptl_crystal_grow_comp> <PDBx:exptl_crystal_grow_comp crystal_id="1" id="5"> <PDBx:sol_id>2</PDBx:sol_id> <PDBx:name>water</PDBx:name> <PDBx:volume>0.700 ml</PDBx:volume> <PDBx:conc>neat</PDBx:conc> <PDBx:details>in 3 mM NaAzide</PDBx:details> </PDBx:exptl_crystal_grow_comp> </PDBx:exptl_crystal_grow_compCategory> The concentration of the solution component. 200 \ml 0.1 ml A description of any special aspects of the solution component. When the solution component is the one that contains the macromolecule, this could be the specification of the buffer in which the macromolecule was stored. When the solution component is a buffer component, this could be the methods (or formula) used to achieve a desired pH. in 3 mM NaAzide The protein solution was in a buffer containing 25 mM NaCl, 100 mM NaMES/MES buffer, pH 7.5, 3 mM NaAzide in 3 mM NaAzide. Buffer components were mixed to produce a pH of 4.7 according to a ratio calculated from the pKa. The actual pH of solution 2 was not measured. A common name for the component of the solution. protein in buffer acetic acid An identifier for the solution to which the given solution component belongs. 1 well solution solution A The volume of the solution component. 200 \ml 0.1 ml The value of attribute id in category exptl_crystal_grow_comp must uniquely identify each item in the EXPTL_CRYSTAL_GROW_COMP list. Note that this item need not be a number; it can be any unique identifier. 1 A protein in buffer This data item is a pointer to attribute id in category exptl_crystal in the EXPTL_CRYSTAL category. Data items in the GEOM and related (GEOM_ANGLE, GEOM_BOND, GEOM_CONTACT, GEOM_HBOND and GEOM_TORSION) categories record details about the molecular and crystal geometry, as calculated from the contents of the ATOM, CELL, and SYMMETRY data. Geometry data are therefore redundant, in that they can be calculated from other more fundamental quantities in the data block. They serve, however, the dual purpose of providing a check on the correctness of both sets of data, and of enabling the most important geometric data to be identified for publication by setting the appropriate publication flag. The description of geometrical information not covered by the existing data names in the GEOM categories, such as least-squares planes. This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the GEOM_ANGLE category record details about the molecular and crystal angles, as calculated from the contents of the ATOM, CELL, and SYMMETRY data. Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. <PDBx:geom_angleCategory> <PDBx:geom_angle atom_site_id_1="C2" atom_site_id_2="O1" atom_site_id_3="C5" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <PDBx:value>111.6(2)</PDBx:value> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_angle> <PDBx:geom_angle atom_site_id_1="O1" atom_site_id_2="C2" atom_site_id_3="C3" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <PDBx:value>110.9(2)</PDBx:value> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_angle> <PDBx:geom_angle atom_site_id_1="O1" atom_site_id_2="C2" atom_site_id_3="O21" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <PDBx:value>122.2(3)</PDBx:value> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_angle> <PDBx:geom_angle atom_site_id_1="C3" atom_site_id_2="C2" atom_site_id_3="O21" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <PDBx:value>127.0(3)</PDBx:value> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_angle> <PDBx:geom_angle atom_site_id_1="C2" atom_site_id_2="C3" atom_site_id_3="N4" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <PDBx:value>101.3(2)</PDBx:value> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_angle> <PDBx:geom_angle atom_site_id_1="C2" atom_site_id_2="C3" atom_site_id_3="C31" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <PDBx:value>111.3(2)</PDBx:value> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_angle> <PDBx:geom_angle atom_site_id_1="C2" atom_site_id_2="C3" atom_site_id_3="H3" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <PDBx:value>107(1)</PDBx:value> </PDBx:geom_angle> <PDBx:geom_angle atom_site_id_1="N4" atom_site_id_2="C3" atom_site_id_3="C31" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <PDBx:value>116.7(2)</PDBx:value> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_angle> </PDBx:geom_angleCategory> An optional identifier of the first of the three atom sites that define the angle specified by attribute value. in category geom_angle This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the three atom sites that define the angle specified by attribute value. in category geom_angle This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the three atom sites that define the angle specified by attribute value. in category geom_angle This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the three atom sites that define the angle specified by attribute value. in category geom_angle This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the three atom sites that define the angle specified by attribute value. in category geom_angle This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the three atom sites that define the angle specified by attribute value. in category geom_angle This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the three atom sites that define the angle specified by attribute value. in category geom_angle This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the three atom sites that define the angle specified by attribute value. in category geom_angle This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the three atom sites that define the angle specified by attribute value. in category geom_angle This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the three atom sites that define the angle specified by attribute value. in category geom_angle This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the three atom sites that define the angle specified by attribute value. in category geom_angle This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the three atom sites that define the angle specified by attribute value. in category geom_angle This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the three atom sites that define the angle specified by attribute value. in category geom_angle This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the three atom sites that define the angle specified by attribute value. in category geom_angle This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the three atom sites that define the angle specified by attribute value. in category geom_angle This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the three atom sites that define the angle specified by attribute value. in category geom_angle This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the three atom sites that define the angle specified by attribute value. in category geom_angle This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the three atom sites that define the angle specified by attribute value. in category geom_angle This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the three atom sites that define the angle specified by attribute value. in category geom_angle This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the three atom sites that define the angle specified by attribute value. in category geom_angle This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the three atom sites that define the angle specified by attribute value. in category geom_angle This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the three atom sites that define the angle specified by attribute value. in category geom_angle This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the three atom sites that define the angle specified by attribute value. in category geom_angle This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the three atom sites that define the angle specified by attribute value. in category geom_angle This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the three atom sites that define the angle specified by attribute value. in category geom_angle This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the three atom sites that define the angle specified by attribute value. in category geom_angle This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the three atom sites that define the angle specified by attribute value. in category geom_angle This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. Pointer to attribute pdbx_PDB_model_num in category atom_site Pointer to attribute pdbx_PDB_ins_code in category atom_site. Pointer to attribute pdbx_PDB_ins_code in category atom_site. Pointer to attribute pdbx_PDB_ins_code in category atom_site. This code signals if the angle is referred to in a publication or should be placed in a table of significant angles. Angle in degrees bounded by the three sites _geom_angle.atom_site_id_1, _geom_angle.atom_site_id_2 and attribute atom_site_id_3 in category geom_angle. The estimated standard deviation of attribute value in category geom_angle. The identifier of the first of the three atom sites that define the angle specified by attribute value. in category geom_angle This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The identifier of the second of the three atom sites that define the angle specified by attribute value in category geom_angle. The second atom is taken to be the apex of the angle. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The identifier of the third of the three atom sites that define the angle specified by attribute value. in category geom_angle This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The symmetry code of the first of the three atom sites that define the angle specified by attribute in category geom_angle. no symmetry or translation to site 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 The symmetry code of the second of the three atom sites that define the angle specified by attribute in category geom_angle. no symmetry or translation to site 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 The symmetry code of the third of the three atom sites that define the angle specified by attribute in category geom_angle. no symmetry or translation to site 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 Data items in the GEOM_BOND category record details about molecular and crystal bonds, as calculated from the contents of the ATOM, CELL, and SYMMETRY data. Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. <PDBx:geom_bondCategory> <PDBx:geom_bond atom_site_id_1="O1" atom_site_id_2="C2" site_symmetry_1="1_555" site_symmetry_2="1_555"> <PDBx:dist>1.342(4)</PDBx:dist> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_bond> <PDBx:geom_bond atom_site_id_1="O1" atom_site_id_2="C5" site_symmetry_1="1_555" site_symmetry_2="1_555"> <PDBx:dist>1.439(3)</PDBx:dist> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_bond> <PDBx:geom_bond atom_site_id_1="C2" atom_site_id_2="C3" site_symmetry_1="1_555" site_symmetry_2="1_555"> <PDBx:dist>1.512(4)</PDBx:dist> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_bond> <PDBx:geom_bond atom_site_id_1="C2" atom_site_id_2="O21" site_symmetry_1="1_555" site_symmetry_2="1_555"> <PDBx:dist>1.199(4)</PDBx:dist> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_bond> <PDBx:geom_bond atom_site_id_1="C3" atom_site_id_2="N4" site_symmetry_1="1_555" site_symmetry_2="1_555"> <PDBx:dist>1.465(3)</PDBx:dist> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_bond> <PDBx:geom_bond atom_site_id_1="C3" atom_site_id_2="C31" site_symmetry_1="1_555" site_symmetry_2="1_555"> <PDBx:dist>1.537(4)</PDBx:dist> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_bond> <PDBx:geom_bond atom_site_id_1="C3" atom_site_id_2="H3" site_symmetry_1="1_555" site_symmetry_2="1_555"> <PDBx:dist>1.00(3)</PDBx:dist> </PDBx:geom_bond> <PDBx:geom_bond atom_site_id_1="N4" atom_site_id_2="C5" site_symmetry_1="1_555" site_symmetry_2="1_555"> <PDBx:dist>1.472(3)</PDBx:dist> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_bond> </PDBx:geom_bondCategory> An optional identifier of the first of the two atom sites that define the bond specified by attribute dist. in category geom_bond This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the bond specified by attribute dist. in category geom_bond This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the bond specified by attribute dist. in category geom_bond This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the bond specified by attribute dist. in category geom_bond This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the bond specified by attribute dist. in category geom_bond This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the bond specified by attribute dist. in category geom_bond This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the bond specified by attribute dist. in category geom_bond This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the bond specified by attribute dist. in category geom_bond This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the bond specified by attribute dist. in category geom_bond This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the bond specified by attribute dist. in category geom_bond This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the bond specified by attribute dist. in category geom_bond This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the bond specified by attribute dist. in category geom_bond This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the bond specified by attribute dist. in category geom_bond This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the bond specified by attribute dist. in category geom_bond This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the bond specified by attribute dist. in category geom_bond This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the bond specified by attribute dist. in category geom_bond This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the bond specified by attribute dist. in category geom_bond This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the bond specified by attribute dist. in category geom_bond This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. The intramolecular bond distance in angstroms. The estimated standard deviation of attribute dist in category geom_bond. Pointer to attribute pdbx_PDB_model_num in category atom_site Pointer to attribute pdbx_PDB_ins_code in category atom_site. Pointer to attribute pdbx_PDB_ins_code in category atom_site. This code signals if the bond distance is referred to in a publication or should be placed in a list of significant bond distances. The identifier of the first of the two atom sites that define the bond specified by attribute dist. in category geom_bond This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The identifier of the second of the two atom sites that define the bond specified by attribute dist. in category geom_bond This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The symmetry code of the first of the two atom sites that define the bond specified by attribute dist in category geom_bond. no symmetry or translation to site 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 The symmetry code of the second of the two atom sites that define the bond specified by attribute dist in category geom_bond. no symmetry or translation to site 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 Data items in the GEOM_CONTACT category record details about molecular and crystal contacts, as calculated from the contents of the ATOM, CELL, and SYMMETRY data. Example 1 - based on data set CLPHO6 of Ferguson, Ruhl, McKervey & Browne (1991). Acta Cryst. C48, 2262-2264]. <PDBx:geom_contactCategory> <PDBx:geom_contact atom_site_id_1="O(1)" atom_site_id_2="O(2)" site_symmetry_1="" site_symmetry_2=""> <PDBx:dist>2.735(3)</PDBx:dist> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_contact> <PDBx:geom_contact atom_site_id_1="H(O1)" atom_site_id_2="O(2)" site_symmetry_1="" site_symmetry_2=""> <PDBx:dist>1.82</PDBx:dist> <PDBx:publ_flag>no</PDBx:publ_flag> </PDBx:geom_contact> </PDBx:geom_contactCategory> An optional identifier of the first of the two atom sites that define the contact specified by attribute dist. in category geom_contact This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the contact specified by attribute dist. in category geom_contact This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the contact specified by attribute dist. in category geom_contact This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the contact specified by attribute dist. in category geom_contact This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the contact specified by attribute dist. in category geom_contact This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the contact specified by attribute dist. in category geom_contact This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the contact specified by attribute dist. in category geom_contact This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the contact specified by attribute dist. in category geom_contact This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the contact specified by attribute dist. in category geom_contact This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the contact specified by attribute dist. in category geom_contact This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the contact specified by attribute dist. in category geom_contact This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the contact specified by attribute dist. in category geom_contact This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the contact specified by attribute dist. in category geom_contact This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the contact specified by attribute dist. in category geom_contact This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the contact specified by attribute dist. in category geom_contact This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the contact specified by attribute dist. in category geom_contact This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the contact specified by attribute dist. in category geom_contact This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the contact specified by attribute dist. in category geom_contact This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. The interatomic contact distance in angstroms. The estimated standard deviation of attribute dist in category geom_contact. Pointer to attribute pdbx_PDB_model_num in category atom_site Pointer to attribute pdbx_PDB_ins_code in category atom_site. Pointer to attribute pdbx_PDB_ins_code in category atom_site. This code signals if the contact distance is referred to in a publication or should be placed in a list of significant contact distances. The identifier of the first of the two atom sites that define the contact specified by attribute dist. in category geom_contact This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The identifier of the second of the two atom sites that define the contact specified by attribute dist. in category geom_contact This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The symmetry code of the first of the two atom sites that define the contact specified by attribute dist in category geom_contact. no symmetry or translation to site 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 The symmetry code of the second of the two atom sites that define the contact specified by attribute dist in category geom_contact. no symmetry or translation to site 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 Data items in the GEOM_HBOND category record details about hydrogen bonds, as calculated from the contents of the ATOM, CELL, and SYMMETRY data. Example 1 - based on C~14~H~13~ClN~2~O.H~2~O, reported by Palmer, Puddle & Lisgarten [(1993). Acta Cryst. C49, 1777-1779]. <PDBx:geom_hbondCategory> <PDBx:geom_hbond atom_site_id_D="N6" atom_site_id_H="HN6" atom_site_id_A="OW"> <PDBx:dist_DH>0.888(8)</PDBx:dist_DH> <PDBx:dist_HA>1.921(12)</PDBx:dist_HA> <PDBx:dist_DA>2.801(8)</PDBx:dist_DA> <PDBx:angle_DHA>169.6(8)</PDBx:angle_DHA> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_hbond> <PDBx:geom_hbond atom_site_id_D="OW" atom_site_id_H="HO2" atom_site_id_A="O7"> <PDBx:dist_DH>0.917(6)</PDBx:dist_DH> <PDBx:dist_HA>1.923(12)</PDBx:dist_HA> <PDBx:dist_DA>2.793(8)</PDBx:dist_DA> <PDBx:angle_DHA>153.5(8)</PDBx:angle_DHA> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_hbond> <PDBx:geom_hbond atom_site_id_D="OW" atom_site_id_H="HO1" atom_site_id_A="N10"> <PDBx:dist_DH>0.894(8)</PDBx:dist_DH> <PDBx:dist_HA>1.886(11)</PDBx:dist_HA> <PDBx:dist_DA>2.842(8)</PDBx:dist_DA> <PDBx:angle_DHA>179.7(9)</PDBx:angle_DHA> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_hbond> </PDBx:geom_hbondCategory> The angle in degrees defined by the donor, hydrogen and acceptor atom sites in a hydrogen bond. The standard uncertainty (e.s.d) of attribute angle_DHA in category geom_hbond. An optional identifier of the acceptor atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the donor atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the hydrogen atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the acceptor atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the donor atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the hydrogen atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the acceptor atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the donor atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the hydrogen atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the acceptor atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the donor atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the hydrogen atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the acceptor atom site that defines the hydrogen bond. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the donor atom site that defines the hydrogen bond. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the hydrogen atom site that defines the hydrogen bond. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the acceptor atom site that defines the hydrogen bond. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the donor atom site that defines the hydrogen bond. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the hydrogen atom site that defines the hydrogen bond. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the acceptor atom site that defines the hydrogen bond. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the donor atom site that defines the hydrogen bond. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the hydrogen atom site that defines the hydrogen bond. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the acceptor atom site that defines the hydrogen bond. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the donor atom site that defines the hydrogen bond. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the hydrogen atom site that defines the hydrogen bond. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the acceptor atom site that defines the hydrogen bond. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the donor atom site that defines the hydrogen bond. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the hydrogen atom site that defines the hydrogen bond. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. The distance in angstroms between the donor and acceptor atom sites in a hydrogen bond. The standard undercertainty (e.s.d) in angstroms of attribute dist_DA in category geom_hbond. The distance in angstroms between the donor and hydrogen atom sites in a hydrogen bond. The standard undercertainty (e.s.d) in angstroms of attribute dist_DH in category geom_hbond. The distance in angstroms between the hydrogen and acceptor atom sites in a hydrogen bond. The standard undercertainty (e.s.d) in angstroms of attribute dist_HA in category geom_hbond. This code signals if the hydrogen bond information is referred to in a publication or should be placed in a table of significant hydrogen-bond geometry. The identifier of the acceptor atom site that defines the hydrogen bond. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The identifier of the donor atom site that defines the hydrogen bond. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The identifier of the hydrogen atom site that defines the hydrogen bond. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The symmetry code of the acceptor atom site that defines the hydrogen bond. no symmetry or translation to site 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 The symmetry code of the donor atom site that defines the hydrogen bond. no symmetry or translation to site 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 The symmetry code of the hydrogen atom site that defines the hydrogen bond. no symmetry or translation to site 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 Data items in the GEOM_TORSION category record details about molecular and crystal torsion angles, as calculated from the contents of the ATOM, CELL, and SYMMETRY data. The vector direction attribute atom_site_id_2 in category geom_torsion to attribute atom_site_id_3 in category geom_torsion is the viewing direction, and the torsion angle is the angle of twist required to superimpose the projection of the vector site2-site1 onto the projection of the vector site3-site4. Clockwise torsions are positive, anticlockwise torsions are negative. Ref: Klyne, W. & Prelog, V. (1960). Experientia, 16, 521-523. Example 3 - based on data set CLPHO6 of Ferguson, Ruhl, McKervey & Browne [(1991). Acta Cryst. C48, 2262-2264]. <PDBx:geom_torsionCategory> <PDBx:geom_torsion atom_site_id_1="C(9)" atom_site_id_2="O(2)" atom_site_id_3="C(7)" atom_site_id_4="C(2)" site_symmetry_1="" site_symmetry_2="" site_symmetry_3="" site_symmetry_4=""> <PDBx:value>71.8</PDBx:value> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_torsion> <PDBx:geom_torsion atom_site_id_1="C(7)" atom_site_id_2="O(2)" atom_site_id_3="C(9)" atom_site_id_4="C(10)" site_symmetry_1="" site_symmetry_2="" site_symmetry_3="" site_symmetry_4="2_666"> <PDBx:value>-168.0</PDBx:value> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_torsion> <PDBx:geom_torsion atom_site_id_1="C(10)" atom_site_id_2="O(3)" atom_site_id_3="C(8)" atom_site_id_4="C(6)" site_symmetry_1="" site_symmetry_2="" site_symmetry_3="" site_symmetry_4=""> <PDBx:value>-167.7</PDBx:value> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_torsion> <PDBx:geom_torsion atom_site_id_1="C(8)" atom_site_id_2="O(3)" atom_site_id_3="C(10)" atom_site_id_4="C(9)" site_symmetry_1="" site_symmetry_2="" site_symmetry_3="" site_symmetry_4="2_666"> <PDBx:value>-69.7</PDBx:value> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_torsion> <PDBx:geom_torsion atom_site_id_1="O(1)" atom_site_id_2="C(1)" atom_site_id_3="C(2)" atom_site_id_4="C(3)" site_symmetry_1="" site_symmetry_2="" site_symmetry_3="" site_symmetry_4=""> <PDBx:value>-179.5</PDBx:value> <PDBx:publ_flag>no</PDBx:publ_flag> </PDBx:geom_torsion> <PDBx:geom_torsion atom_site_id_1="O(1)" atom_site_id_2="C(1)" atom_site_id_3="C(2)" atom_site_id_4="C(7)" site_symmetry_1="" site_symmetry_2="" site_symmetry_3="" site_symmetry_4=""> <PDBx:value>-0.6</PDBx:value> <PDBx:publ_flag>no</PDBx:publ_flag> </PDBx:geom_torsion> </PDBx:geom_torsionCategory> An optional identifier of the first of the four atom sites that define the torsion angle specified by attribute value. in category geom_torsion This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the four atom sites that define the torsion angle specified by attribute value. in category geom_torsion This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the four atom sites that define the torsion angle specified by attribute value. in category geom_torsion This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the fourth of the four atom sites that define the torsion angle specified by attribute value. in category geom_torsion This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the four atom sites that define the torsion angle specified by attribute value. in category geom_torsion This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the four atom sites that define the torsion angle specified by attribute value. in category geom_torsion This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the four atom sites that define the torsion angle specified by attribute value. in category geom_torsion This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the fourth of the four atom sites that define the torsion angle specified by attribute value. in category geom_torsion This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the four atom sites that define the torsion angle specified by attribute value. in category geom_torsion This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the four atom sites that define the torsion angle specified by attribute value. in category geom_torsion This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the four atom sites that define the torsion angle specified by attribute value. in category geom_torsion This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the fourth of the four atom sites that define the torsion angle specified by attribute value. in category geom_torsion This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the four atom sites that define the torsion angle specified by attribute value. in category geom_torsion This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the four atom sites that define the torsion angle specified by attribute value. in category geom_torsion This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the four atom sites that define the torsion angle specified by attribute value. in category geom_torsion This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the fourth of the four atom sites that define the torsion angle specified by attribute value. in category geom_torsion This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the four atom sites that define the torsion angle specified by attribute value. in category geom_torsion This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the four atom sites that define the torsion angle specified by attribute value. in category geom_torsion This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the four atom sites that define the torsion angle specified by attribute value. in category geom_torsion This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the fourth of the four atom sites that define the torsion angle specified by attribute value. in category geom_torsion This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the four atom sites that define the torsion angle specified by attribute value. in category geom_torsion This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the four atom sites that define the torsion angle specified by attribute value. in category geom_torsion This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the four atom sites that define the torsion angle specified by attribute value. in category geom_torsion This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the fourth of the four atom sites that define the torsion angle specified by attribute value. in category geom_torsion This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the four atom sites that define the torsion angle specified by attribute value. in category geom_torsion This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the four atom sites that define the torsion angle specified by attribute value. in category geom_torsion This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the four atom sites that define the torsion angle specified by attribute value. in category geom_torsion This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the fourth of the four atom sites that define the torsion angle specified by attribute value. in category geom_torsion This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the four atom sites that define the torsion angle specified by attribute value. in category geom_torsion This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the four atom sites that define the torsion angle specified by attribute value. in category geom_torsion This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the four atom sites that define the torsion angle specified by attribute value. in category geom_torsion This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the fourth of the four atom sites that define the torsion angle specified by attribute value. in category geom_torsion This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the four atom sites that define the torsion angle specified by attribute value. in category geom_torsion This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the four atom sites that define the torsion angle specified by attribute value. in category geom_torsion This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the four atom sites that define the torsion angle specified by attribute value. in category geom_torsion This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the fourth of the four atom sites that define the torsion angle specified by attribute value. in category geom_torsion This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. Pointer to attribute pdbx_PDB_model_num in category atom_site Pointer to attribute pdbx_PDB_ins_code in category atom_site. Pointer to attribute pdbx_PDB_ins_code in category atom_site. Pointer to attribute pdbx_PDB_ins_code in category atom_site. Pointer to attribute pdbx_PDB_ins_code in category atom_site. This code signals if the torsion angle is referred to in a publication or should be placed in a table of significant torsion angles. The value of the torsion angle in degrees. The estimated standard deviation of attribute value in category geom_torsion. The identifier of the first of the four atom sites that define the torsion angle specified by attribute value. in category geom_torsion This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The identifier of the second of the four atom sites that define the torsion angle specified by attribute value. in category geom_torsion This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The identifier of the third of the four atom sites that define the torsion angle specified by attribute value. in category geom_torsion This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The identifier of the fourth of the four atom sites that define the torsion angle specified by attribute value. in category geom_torsion This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The symmetry code of the first of the four atom sites that define the torsion angle specified by attribute value in category geom_torsion. no symmetry or translation to site 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 The symmetry code of the second of the four atom sites that define the torsion angle specified by attribute value in category geom_torsion. no symmetry or translation to site 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 The symmetry code of the third of the four atom sites that define the torsion angle specified by attribute value in category geom_torsion. no symmetry or translation to site 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 The symmetry code of the fourth of the four atom sites that define the torsion angle specified by attribute value in category geom_torsion. no symmetry or translation to site 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 Data items in the JOURNAL category record details about the book keeping entries used by the journal's staff when processing a data block submitted for publication. Normally the creator of a data block will not specify these data. The data names are not defined in the dictionary because they are for journal use only. Example 1 - based on Acta Cryst. file for entry HL0007 [Willis, Beckwith & Tozer (1991). Acta Cryst. C47, 2276-2277]. <PDBx:journalCategory> <PDBx:journal entry_id="TOZ"> <PDBx:date_recd_electronic>1991-04-15</PDBx:date_recd_electronic> <PDBx:date_from_coeditor>1991-04-18</PDBx:date_from_coeditor> <PDBx:date_accepted>1991-04-18</PDBx:date_accepted> <PDBx:date_printers_first>1991-08-07</PDBx:date_printers_first> <PDBx:date_proofs_out>1991-08-07</PDBx:date_proofs_out> <PDBx:coeditor_code>HL0007</PDBx:coeditor_code> <PDBx:techeditor_code>C910963</PDBx:techeditor_code> <PDBx:coden_ASTM>ACSCEE</PDBx:coden_ASTM> <PDBx:name_full>Acta Crystallographica Section C</PDBx:name_full> <PDBx:year>1991</PDBx:year> <PDBx:volume>47</PDBx:volume> <PDBx:issue>NOV91</PDBx:issue> <PDBx:page_first>2276</PDBx:page_first> <PDBx:page_last>2277</PDBx:page_last> </PDBx:journal> </PDBx:journalCategory> Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the JOURNAL_INDEX category are used to list terms employed in generating the journal indexes. Normally the creator of a data block will not specify these data items. Example 1 - based on a paper by Zhu, Reynolds, Klein & Trudell [(1994). Acta Cryst. C50, 2067-2069]. <PDBx:journal_indexCategory> <PDBx:journal_index type="S" term="alkaloids"> <PDBx:subterm>(-)-norcocaine</PDBx:subterm> </PDBx:journal_index> </PDBx:journal_indexCategory> Journal index data items are defined by the journal staff. Journal index data items are defined by the journal staff. Journal index data items are defined by the journal staff. Placeholder category for PDB coordinate data. Data items in the NDB_STRUCT_CONF_NA category describes secondary structure features in this entry. This data item counts the number of occurences of this feature in this entry. This data item is a pointer to attribute id in category entry in the ENTRY category. This data item identifies a secondary structure feature of this entry. Data items in the NDB_STRUCT_FEATURE_NA category describes tertiary and other special structural features in this entry. This data item counts the number of occurences of this feature in this entry. This data item is a pointer to attribute id in category entry in the ENTRY category. This data item identifies a structural feature of this entry. Data items in the NDB_STRUCT_NA_BASE_PAIR category record details of base pairing interactions. <PDBx:ndb_struct_na_base_pairCategory> <PDBx:ndb_struct_na_base_pair model_number="1" i_label_comp_id="G" i_label_asym_id="A" i_label_seq_id="1" i_symmetry="1_555" j_label_comp_id="C" j_label_asym_id="A" j_label_seq_id="8" j_symmetry="7_555"> <PDBx:shear>-0.396</PDBx:shear> <PDBx:stretch>-0.156</PDBx:stretch> <PDBx:stagger>-0.018</PDBx:stagger> <PDBx:buckle>-5.523</PDBx:buckle> <PDBx:propeller>-6.752</PDBx:propeller> <PDBx:opening>-3.291</PDBx:opening> </PDBx:ndb_struct_na_base_pair> <PDBx:ndb_struct_na_base_pair model_number="1" i_label_comp_id="G" i_label_asym_id="A" i_label_seq_id="2" i_symmetry="1_555" j_label_comp_id="C" j_label_asym_id="A" j_label_seq_id="7" j_symmetry="7_555"> <PDBx:shear>-0.094</PDBx:shear> <PDBx:stretch>-0.220</PDBx:stretch> <PDBx:stagger>-0.334</PDBx:stagger> <PDBx:buckle>-4.727</PDBx:buckle> <PDBx:propeller>-9.765</PDBx:propeller> <PDBx:opening>2.311</PDBx:opening> </PDBx:ndb_struct_na_base_pair> <PDBx:ndb_struct_na_base_pair model_number="1" i_label_comp_id="G" i_label_asym_id="A" i_label_seq_id="3" i_symmetry="1_555" j_label_comp_id="C" j_label_asym_id="A" j_label_seq_id="6" j_symmetry="7_555"> <PDBx:shear>-0.285</PDBx:shear> <PDBx:stretch>-0.239</PDBx:stretch> <PDBx:stagger>0.008</PDBx:stagger> <PDBx:buckle>-6.454</PDBx:buckle> <PDBx:propeller>-12.575</PDBx:propeller> <PDBx:opening>-1.181</PDBx:opening> </PDBx:ndb_struct_na_base_pair> </PDBx:ndb_struct_na_base_pairCategory> The value of the base pair buckle parameter. Base pair classification of Westhoff and Leontis. Base pair classification of Saenger Describes the PDB insertion code of the i-th base in the base pair. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. Describes the asym id of the i-th base in the base pair. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Describes the sequence number of the i-th base in the base pair. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. Describes the PDB insertion code of the j-th base in the base pair. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. Describes the asym id of the j-th base in the base pair. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Describes the sequence number of the j-th base in the base pair. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. The value of the base pair opening parameter. Text label for this base pair. Sequential number of pair in the pair sequence. The value of the base pair propeller parameter. The value of the base pair shear parameter. The value of the base pair stagger parameter. The value of the base pair stretch parameter. Describes the model number of the the base pair. This data item is a pointer to attribute ndb_model in category atom_site in the ATOM_SITE category. Describes the component id of the i-th base in the base pair. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. Describes the asym id of the i-th base in the base pair. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. Describes the sequence number of the i-th base in the base pair. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. Describes the symmetry operation that should be applied to the coordinates of the i-th base to generate the first partner in the base pair. no symmetry or translation to site 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 Describes the component id of the j-th base in the base pair. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. Describes the asym id of the j-th base in the base pair. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. Describes the sequence number of the j-th base in the base pair. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. Describes the symmetry operation that should be applied to the coordinates of the j-th base to generate the second partner in the base pair. no symmetry or translation to site 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 Data items in the NDB_STRUCT_NA_BASE_PAIR_STEP category record details of base pair step interactions. <PDBx:ndb_struct_na_base_pair_stepCategory> <PDBx:ndb_struct_na_base_pair_step model_number="1" i_label_comp_id_1="G" i_label_asym_id_1="A" i_label_seq_id_1="1" i_symmetry_1="1_555" j_label_comp_id_1="C" j_label_asym_id_1="A" j_label_seq_id_1="8" j_symmetry_1="7_555" i_label_comp_id_2="G" i_label_asym_id_2="A" i_label_seq_id_2="2" i_symmetry_2="1_555" j_label_comp_id_2="C" j_label_asym_id_2="A" j_label_seq_id_2="7" j_symmetry_2="7_555"> <PDBx:shift>0.369</PDBx:shift> <PDBx:slide>-1.414</PDBx:slide> <PDBx:rise>3.339</PDBx:rise> <PDBx:tilt>3.056</PDBx:tilt> <PDBx:roll>9.755</PDBx:roll> <PDBx:twist>33.530</PDBx:twist> </PDBx:ndb_struct_na_base_pair_step> <PDBx:ndb_struct_na_base_pair_step model_number="1" i_label_comp_id_1="G" i_label_asym_id_1="A" i_label_seq_id_1="2" i_symmetry_1="1_555" j_label_comp_id_1="C" j_label_asym_id_1="A" j_label_seq_id_1="7" j_symmetry_1="7_555" i_label_comp_id_2="G" i_label_asym_id_2="A" i_label_seq_id_2="3" i_symmetry_2="1_555" j_label_comp_id_2="C" j_label_asym_id_2="A" j_label_seq_id_2="6" j_symmetry_2="7_555"> <PDBx:shift>0.176</PDBx:shift> <PDBx:slide>-1.672</PDBx:slide> <PDBx:rise>3.371</PDBx:rise> <PDBx:tilt>-1.176</PDBx:tilt> <PDBx:roll>6.725</PDBx:roll> <PDBx:twist>30.004</PDBx:twist> </PDBx:ndb_struct_na_base_pair_step> </PDBx:ndb_struct_na_base_pair_stepCategory> The value of the base pair step helical rise parameter. The value of the base pair step helical twist parameter. Describes the PDB insertion code of the i-th base in the first base pair of the step. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. Describes the PDB insertion code of the i-th base in the second base pair of the step. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. Describes the author's asym id of the i-th base in the first base pair of the step. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Describes the author's asym id of the i-th base in the second base pair of the step. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Describes the author's sequence number of the i-th base in the first base pair of the step. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. Describes the author's sequence number of the i-th base in the second base pair of the step. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. The value of the base pair step inclination parameter. Describes the PDB insertion code of the j-th base in the first base pair of the step. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. Describes the PDB insertion code of the j-th base in the second base pair of the step. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. Describes the author's asym id of the j-th base in the first base pair of the step. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Describes the author's asym id of the j-th base in the second base pair of the step. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Describes the author's sequence number of the j-th base in the first base pair of the step. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. Describes the author's sequence number of the j-th base in the second base pair of the step. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. The value of the base pair step rise parameter. The value of the base pair step roll parameter. The value of the base pair step shift parameter. The value of the base pair step slide parameter. The text name of this step. The sequence number of this step in the step sequence. The value of the base pair step tilt parameter. The value of the base pair step twist parameter. The value of the base pair step twist parameter. The value of the base pair step X displacement parameter. The value of the base pair step Y displacement parameter. Describes the model number of the the base pair step. This data item is a pointer to attribute ndb_model in category atom_site in the ATOM_SITE category. Describes the component id of the i-th base in the first base pair of the step. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. Describes the asym id of the i-th base in the first base pair of the step. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. Describes the sequence number of the i-th base in the first base pair of the step. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. Describes the symmetry operation that should be applied to the coordinates of the i-th base to generate the first partner in the first base pair of the step. no symmetry or translation to site 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 Describes the component id of the j-th base in the first base pair of the step. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. Describes the asym id of the j-th base in the first base pair of the step. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. Describes the sequence number of the j-th base in the first base pair of the step. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. Describes the symmetry operation that should be applied to the coordinates of the j-th base to generate the second partner in the first base pair of the step. no symmetry or translation to site 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 Describes the component id of the i-th base in the second base pair of the step. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. Describes the asym id of the i-th base in the second base pair of the step. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. Describes the sequence number of the i-th base in the second base pair of the step. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. Describes the symmetry operation that should be applied to the coordinates of the i-th base to generate the first partner in the second base pair of the step. no symmetry or translation to site 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 Describes the component id of the j-th base in the second base pair of the step. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. Describes the asym id of the j-th base in the second base pair of the step. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. Describes the sequence number of the j-th base in the second base pair of the step. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. Describes the symmetry operation that should be applied to the coordinates of the j-th base to generate the second partner in the second base pair of the step. no symmetry or translation to site 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 The PDBX_AUDIT holds current version information. The value of attribute entry_id in category pdbx_audit identifies the data block. 1 The value of attribute entry_id in category pdbx_audit identifies the data block. BDL001 Data items in the PDBX_AUDIT_AUTHOR category record details about the author(s) of the data block. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:pdbx_audit_authorCategory> <PDBx:pdbx_audit_author ordinal="1"> <PDBx:name>Fitzgerald, Paula M.D.</PDBx:name> <PDBx:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</PDBx:address> </PDBx:pdbx_audit_author> <PDBx:pdbx_audit_author ordinal="2"> <PDBx:name>McKeever, Brian M.</PDBx:name> <PDBx:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</PDBx:address> </PDBx:pdbx_audit_author> <PDBx:pdbx_audit_author ordinal="3"> <PDBx:name>Van Middlesworth, J.F.</PDBx:name> <PDBx:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</PDBx:address> </PDBx:pdbx_audit_author> <PDBx:pdbx_audit_author ordinal="4"> <PDBx:name>Springer, James P.</PDBx:name> <PDBx:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</PDBx:address> </PDBx:pdbx_audit_author> </PDBx:pdbx_audit_authorCategory> The address of an author of this data block. If there are multiple authors, attribute address in category pdbx_audit_author is looped with attribute name in category pdbx_audit_author. Department Institute Street City and postcode COUNTRY The name of an author of this data block. If there are multiple authors, _pdbx_audit_author.name is looped with _pdbx_audit_author.address. The family name(s), followed by a comma and including any dynastic compoents, precedes the first name(s) or initial(s). Bleary, Percival R. O'Neil, F.K. Van den Bossche, G. Yang, D.-L. Simonov, Yu.A A unique sequential integer identifier for each author. 1 2 3 Data items in the PDBX_BUFFER category record details of the sample buffer. Any additional details to do with buffer. aerated The name of each buffer. Acetic acid The value of attribute id in category pdbx_buffer must uniquely identify the sample buffer. Constituents of buffer in sample Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:pdbx_buffer_componentsCategory> <PDBx:pdbx_buffer_components buffer_id="1" id="1"> <PDBx:name>NaCl</PDBx:name> <PDBx:volume>0.200 </PDBx:volume> <PDBx:conc>4 </PDBx:conc> </PDBx:pdbx_buffer_components> <PDBx:pdbx_buffer_components buffer_id="1" id="2"> <PDBx:name>Acetic Acid</PDBx:name> <PDBx:volume>0.047 </PDBx:volume> <PDBx:conc>100</PDBx:conc> </PDBx:pdbx_buffer_components> <PDBx:pdbx_buffer_components buffer_id="1" id="3"> <PDBx:name>water</PDBx:name> <PDBx:volume>0.700 </PDBx:volume> <PDBx:conc>neat</PDBx:conc> </PDBx:pdbx_buffer_components> </PDBx:pdbx_buffer_componentsCategory> The millimolar concentration of buffer component. 200 The concentration units of the component. mg/mL for mg per milliliter mM for millimolar % for percent by volume Any additional details to do with buffer composition. pH adjusted with NaOH The isotopic composition of each component, including the % labeling level, if known. For example: 1. Uniform (random) labeling with 15N: U-15N 2. Uniform (random) labeling with 13C, 15N at known labeling levels: U-95% 13C;U-98% 15N 3. Residue selective labeling: U-95% 15N-Thymine 4. Site specific labeling: 95% 13C-Ala18, 5. Natural abundance labeling in an otherwise uniformly labled biomolecule is designated by NA: U-13C; NA-K,H The name of each buffer component. Acetic acid The volume of buffer component. 0.200 This data item is a pointer to attribute id in category pdbx_buffer in the BUFFER category. The value of attribute id in category pdbx_buffer_components must uniquely identify a component of the buffer. Data items in the PDBX_CONSTRUCT category specify a sequence of nucleic acids or amino acids. It is a catch-all that may be used to provide details of sequences known to be relevant to the project as well as primers, plasmids, proteins and such like that are either used or produced during the protein production process. Molecules described here are not necessarily complete, so for instance it would be possible to include either a complete plasmid or just its insert. This category may be considered as an abbreviated form of _entity where the molecules described are not required to appear in the final co-ordinates. Note that the details provided here all pertain to a single entry as defined at deposition. It is anticipated that attribute id in category pdbx_construct would also be composed of a sequence that is unique within a given site prefixed by a code that identifies that site and would, therefore, be GLOBALLY unique. Thus this category could also be used locally to store details about the different constructs used during protein production without reference to the entry_id (which only becomes a meaningful concept during deposition). Example 1 - hypothetical example <PDBx:pdbx_constructCategory> <PDBx:pdbx_construct id="1"> <PDBx:entry_id>111000111</PDBx:entry_id> <PDBx:type>DNA</PDBx:type> <PDBx:entity_id>1</PDBx:entity_id> <PDBx:seq> gatgctgtag gcataggctt ggttatgccg gtactgccgg gcctcttgcg ggatatcgtc gctcaaggcg cactcccgtt ctggataatg ttttttgcgc cgacatcata acggttctgg caaatattct gaaatgagct gttgacaatt aatcatcgat aagcttcttg # - - - - data truncated for brevity - - - -</PDBx:seq> </PDBx:pdbx_construct> </PDBx:pdbx_constructCategory> The primary function of the construct. This should be considered as a guideline only. The date that the sequence was determined. 2003-12-25 2003-12-25:09:00 Additional details about the construct that cannot be represented in the category attribute in category pdbx_construct_feature. In cases where the construct IS found in the co-ordinates then this item provides a pointer to attribute id in category entity in the ENTITY category for the corresponding molecule. The value of attribute entry_id in category pdbx_construct uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to attribute id in category entry. This item may be a site dependent bar code. attribute name in category pdbx_construct provides a placeholder for the local name of the construct, for example the plasmid name if this category is used to list plasmids. attribute organisation in category pdbx_construct describes the organisation in which the attribute id in category pdbx_construct is unique. This will normally be the lab in which the constrcut originated. It is envisaged that this item will permit a globally unique identifier to be constructed in cases where this is not possible from the attribute id in category pdbx_construct alone. In cases where the sequence has been determined by a robot this data item provides a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category for the robot responsible sequence expressed as string of one-letter base codes or one letter amino acid codes. Unusual residues may be represented either using the appropriate one letter code wild cards or by the three letter code in parentheses. gatgctgtag gcataggctt ggttatgccg gtactgccgg gcctcttgcg ggatatcgtc gctcaaggcg cactcccgtt ctggataatg ttttttgcgc cgacatcata acggttctgg caaatattct gaaatgagct gttgacaatt aatcatcgat aagcttcttg The type of nucleic acid sequence in the construct. Note that to find all the DNA molecules it is necessary to search for DNA + cDNA and for RNA, RNA + mRNA + tRNA. The value of attribute id in category pdbx_construct must uniquely identify a record in the PDBX_CONSTRUCT list and should be arranged so that it is composed of a site-speicific prefix combined with a value that is unique within a given site.Note that this item need not be a number; it can be any unique identifier. Data items in the PDBX_CONSTRUCT_FEATURE category may be used to specify various properties of a nucleic acid sequence used during protein production. Example 1 - vector pUC28 <PDBx:pdbx_construct_featureCategory> <PDBx:pdbx_construct_feature id="1" construct_id="1"> <PDBx:entry_id>111000111</PDBx:entry_id> <PDBx:details>pKK84-1 ClaI 5260bp 5247..5247 ptac11 TaqI-TaqI 192bp, -35 trp promoter -&gt; pEA300 5452bp</PDBx:details> </PDBx:pdbx_construct_feature> <PDBx:pdbx_construct_feature id="2" construct_id="1"> <PDBx:entry_id>111000111</PDBx:entry_id> <PDBx:details>pKK84-1 1..5246 5246bp ClaI = AT^CGAT TaqI = T^CGA cgact...</PDBx:details> </PDBx:pdbx_construct_feature> <PDBx:pdbx_construct_feature id="3" construct_id="1"> <PDBx:entry_id>111000111</PDBx:entry_id> <PDBx:start_seq>5247</PDBx:start_seq> <PDBx:end_seq>5436</PDBx:end_seq> <PDBx:details>ptac11 190bp ...cat TaqI = T^CGA ClaI = AT^CGAT</PDBx:details> </PDBx:pdbx_construct_feature> <PDBx:pdbx_construct_feature id="4" construct_id="1"> <PDBx:entry_id>111000111</PDBx:entry_id> <PDBx:start_seq>5437</PDBx:start_seq> <PDBx:end_seq>5450</PDBx:end_seq> <PDBx:details>pKK84-1 5247..5260 14bp</PDBx:details> </PDBx:pdbx_construct_feature> <PDBx:pdbx_construct_feature id="5" construct_id="1"> <PDBx:entry_id>111000111</PDBx:entry_id> <PDBx:type>misc_binding</PDBx:type> <PDBx:details>SIT unique EcoRI-ClaI-HindIII-BamHI-PvuII</PDBx:details> </PDBx:pdbx_construct_feature> <PDBx:pdbx_construct_feature id="6" construct_id="1"> <PDBx:entry_id>111000111</PDBx:entry_id> <PDBx:type>rep_origin</PDBx:type> <PDBx:details>ORI E. coli pMB1 (ColE1 and pBR322)</PDBx:details> </PDBx:pdbx_construct_feature> <PDBx:pdbx_construct_feature id="7" construct_id="1"> <PDBx:entry_id>111000111</PDBx:entry_id> <PDBx:type>promoter</PDBx:type> <PDBx:details>PRO E. coli trp</PDBx:details> </PDBx:pdbx_construct_feature> <PDBx:pdbx_construct_feature id="8" construct_id="1"> <PDBx:entry_id>111000111</PDBx:entry_id> <PDBx:type>CDS</PDBx:type> <PDBx:details>ANT E. coli beta-lactamase gene (bla) ampicillin resistance gene (apr/amp)</PDBx:details> </PDBx:pdbx_construct_feature> </PDBx:pdbx_construct_featureCategory> Details that describe the feature The sequence position at which the feature ends The value of attribute entry_id in category pdbx_construct_feature uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to attribute id in category entry. This item may be a site dependent bar code. The sequence position at which the feature begins The type of the feature The value of attribute construct_id in category pdbx_construct_feature uniquely identifies the construct with which the feature is associated. This is a pointer to attribute id in category pdbx_construct This item may be a site dependent bar code. The value of attribute id in category pdbx_construct_feature must uniquely identify a record in the PDBX_CONSTRUCT_FEATURE list. Note that this item need not be a number; it can be any unique identifier. The PDBX_DATABASE_PDB_OBS_SPR category provides placeholders for information on obsolete/superseded PDB entries The date of replacement. 1997-03-30 Identifier for the type of obsolete entry to be added to this entry. OBSLTE The new PDB identifier for the replaced entry. 2ABC The PDB identifier for the replaced (OLD) entry. 3ABC The PDBX_DATABASE_MESSAGE category provides information about correspondance related to a structure deposition. This code defines the content of the message. This is the date when a message was sent or received. The text of the message. Defines how the message was sent or received. The name of the receiver. The email address of the receiver. The FAX phone number of the receiver. The postal address of the receiver. The phone number of the receiver. The name of the sender. The email address of the sender. The FAX phone number of the sender. The postal address of the sender. The phone number of the sender. This is an unique and sequential identifier for a message. message 1 The value of attribute entry_id in category pdbx_database_message identifies the data block. BDL001 Internal records to track the data processing cycle. <PDBx:pdbx_database_procCategory> <PDBx:pdbx_database_proc entry_id="BDL001" cycle_id="1"> <PDBx:date_begin_cycle>1998-02-27</PDBx:date_begin_cycle> <PDBx:date_end_cycle>1998-02-27</PDBx:date_end_cycle> </PDBx:pdbx_database_proc> </PDBx:pdbx_database_procCategory> This is the date of the start of the processing cycle. 1983-02-27 This is the date of the end of the processing cycle. 1983-02-27 Special details about the current processing cycle. This is a number of the processing cycle. 1 for the initial cycle The value of attribute entry_id in category pdbx_database_proc identifies the data block. BDL001 Data items in PDBX_DATABASE_RELATED contain references to entries that are related to the this entry. <PDBx:pdbx_database_relatedCategory> <PDBx:pdbx_database_related db_name="PDB" db_id="1ABC"></PDBx:pdbx_database_related> </PDBx:pdbx_database_relatedCategory> The identifying content type of the related entry. minimized average structure representative structure ensemble derivative structure native structure other A description of the related entry. 1ABC contains the same protein complexed with Netropsin. The name of the database containing the related entry. PDB - Protein Databank NDB - Nucleic Acid Database BMRB - BioMagResBank BMCD - Biological Macromolecule Crystallization Database The identifying code in the related database. 1ABC BDL001 Data items in the PDBX_DATABASE_REMARK category record keep additional information about the entry. They are mostly used to create 'non-standard' PDB REMARK annotations (6-99). Example 1 - based on PDB entry 1ABC <PDBx:pdbx_database_remarkCategory> <PDBx:pdbx_database_remark id="1"> <PDBx:text> THE NON-CRYSTALLOGRAPHIC RELATIONSHIP BETWEEN THE THREE DOUBLE HELICES IN THE ASYMMETRIC UNIT IS DESCRIBED IN THE MTRIX1-3 RECORDS.</PDBx:text> </PDBx:pdbx_database_remark> </PDBx:pdbx_database_remarkCategory> The full text of the PDB remark record. A unique identifier for the PDB remark record. These are internal RCSB records to keep track of data processing and status of the entry. <PDBx:pdbx_database_statusCategory> <PDBx:pdbx_database_status entry_id="1ABC"> <PDBx:status_code>REL</PDBx:status_code> <PDBx:author_release_status_code>REL</PDBx:author_release_status_code> <PDBx:deposit_site>RCSB</PDBx:deposit_site> <PDBx:process_site>RCSB</PDBx:process_site> <PDBx:recvd_initial_deposition_date>1996-02-13</PDBx:recvd_initial_deposition_date> <PDBx:date_author_approval>1996-02-13</PDBx:date_author_approval> <PDBx:recvd_author_approval>Y</PDBx:recvd_author_approval> <PDBx:author_approval_type>explicit</PDBx:author_approval_type> <PDBx:hold_for_publication>N</PDBx:hold_for_publication> <PDBx:date_hold_coordinates>1996-02-13</PDBx:date_hold_coordinates> <PDBx:date_hold_struct_fact>1996-02-13</PDBx:date_hold_struct_fact> <PDBx:date_of_PDB_release>1996-02-14</PDBx:date_of_PDB_release> <PDBx:date_deposition_form>1996-02-13</PDBx:date_deposition_form> <PDBx:date_coordinates>1996-02-13</PDBx:date_coordinates> <PDBx:date_struct_fact>1996-02-13</PDBx:date_struct_fact> <PDBx:date_manuscript>1996-02-13</PDBx:date_manuscript> <PDBx:recvd_deposit_form>Y</PDBx:recvd_deposit_form> <PDBx:recvd_coordinates>Y</PDBx:recvd_coordinates> <PDBx:recvd_struct_fact>Y</PDBx:recvd_struct_fact> <PDBx:recvd_manuscript>Y</PDBx:recvd_manuscript> <PDBx:recvd_nmr_constraints>N</PDBx:recvd_nmr_constraints> </PDBx:pdbx_database_status> </PDBx:pdbx_database_statusCategory> This code indicates whether the author's approval for an entry was received explicitly or implicitly. The latter is automatically implied by failure to respond to the validation summary within the prescribed period. implicit = automatic approval by failure to acknowledge explicit = approval via depositor acknowledgement The release status authorized by the depositor. REL = Release HOLD = On hold until yyyy-mm-dd HPUB = On hold until publication OBS = Entry has been obsoleted and replaced by another entry WDRN = Entry has been withdrawn by depositor The date the author's approval is received. 1983-02-20 The date the coordinates are received. 1983-02-21 The date the deposition form is received. 1982-02-21 At an author's request, a coordinate entry may be held after processing for some period of time. 1983-02-28 At an author's request, the NMR constraint data may be held after processing for some period of time. 1983-02-28 At an author's request, the structure factors may be held after processing for some period of time. 1983-02-28 The date the manuscript is received. 1983-02-28 The date the structure factors are received. 1983-02-28 PDB release date. This is the date that appears in the PDB REVDAT record. 1983-02-28 The date the structure factors are received. 1983-02-28 The date of complete deposition. This corresponds to the date at which the PDB identifier is assigned. 1983-02-20 The deposited coordinates for this deposition will be released according the value of this item. RELEASE NOW = Release immediately HOLD FOR PUBLICATION = Hold until the primary citation is published HOLD FOR 6 MONTHS = Hold for 6 months HOLD FOR 1 YEAR = Hold for 1 year The deposited NMR constrait data for this deposition will be released according the value of this item. RELEASE NOW = Release immediately HOLD FOR PUBLICATION = Hold until the primary citation is published HOLD FOR 6 MONTHS = Hold for 6 months HOLD FOR 1 YEAR = Hold for 1 year The sequence information for this deposition will be released according the value of this item. Setting this status code to "RELEASE NOW" indicates that the macromolecular sequence(s) for this entry may be displayed in PDB status reports prior to the release of the entry. Setting this status code to "HOLD FOR RELEASE" conceals the sequence information in PDB status reports until the coordinate data for this entry are released. RELEASE NOW = Release sequence information in status reports immediately HOLD FOR RELEASE = Conceal sequence information in status reports until coordinate data is release The deposited structure factors for this deposition will be released according the value of this item. RELEASE NOW = Release immediately HOLD FOR PUBLICATION = Hold until the primary citation is published HOLD FOR 6 MONTHS = Hold for 6 months HOLD FOR 1 YEAR = Hold for 1 year The site where the file was deposited. NDB RCSB PDB EBI OSAKA BNL At an author's request, an entry is to be held until publication. Y The last name of the depositor to be used in correspondance. Smith This is the date when PDB received the author's approval for an entry which has been processed by NDB. (This is a place holder for entries processed before Jan. 1, 1996.) 1983-02-27 The site where the file was deposited. NDB RCSB EBI OSAKA PDB PRAGUE The initials of the annotator processing this entry. BS SJ KB This code indicates whether the author's approval for an entry has been received. Y This code indicates whether the coordinates for an entry have been received. Y This code indicates whether the deposition form for an entry has been received. Y The date of initial deposition. (The first message for deposition has been received.) 1983-02-21 This code indicates whether the internal approval for an entry have been received. Y This code indicates whether the manuscript for an entry has been received. Y This code indicates whether the NMR contraint data for an entry have been received. Y This code indicates whether the structure factors for an entry have been received. Y Code for status of file. REL HOLD REV BIB The value of attribute entry_id in category pdbx_database_status identifies the data block. BDL001 The PDBX_ENTITY_ASSEMBLY category provides a chemical description of the biological assembly studied in terms of its constituent entities. A complex composed of one copy of entities 1 and 2. <PDBx:pdbx_entity_assemblyCategory> <PDBx:pdbx_entity_assembly id="1" entity_id="1"> <PDBx:biol_id>1</PDBx:biol_id> <PDBx:num_copies>1</PDBx:num_copies> </PDBx:pdbx_entity_assembly> <PDBx:pdbx_entity_assembly id="1" entity_id="2"> <PDBx:biol_id>1</PDBx:biol_id> <PDBx:num_copies>1</PDBx:num_copies> </PDBx:pdbx_entity_assembly> </PDBx:pdbx_entity_assemblyCategory> An identifier for the assembly. The number of copies of this entity in the assembly. An identifier for the assembly. An enity identifier. A reference to attribute id in category entity. The PDBX_ENTITY_NAME records additional name information for each entity. Example 1 - <PDBx:pdbx_entity_nameCategory> <PDBx:pdbx_entity_name entity_id="1" name="PLASTOCYANIN" name_type="SWS-NAME"></PDBx:pdbx_entity_name> <PDBx:pdbx_entity_name entity_id="1" name="Electron transport" name_type="SWS-KEYWORD"></PDBx:pdbx_entity_name> </PDBx:pdbx_entity_nameCategory> Pointer to attribute id in category entity. Entity name. Entity name type. Example 1 - This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. A name for the non-polymer entity This data item is a pointer to attribute id in category entity in the ENTITY category. This category contains details of protein characterisation. It refers to the characteristion of the product of a specific step. The date of characterisation step. 2003-12-25 2003-12-25:09:00 Any details associated with this method of protein characterisation. The method used for protein characterisation. Dynamic light scattering Mass spectrometry The result from this method of protein characterisation. This data item is a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category. The value of attribute entry_id in category pdbx_entity_src_gen_character uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to attribute id in category entry. This item may be a site dependent bar code. The value of attribute entity_id in category pdbx_entity_src_gen_character uniquely identifies each protein contained in the project target complex proteins whose structure is to be determined. This data item is a pointer to attribute id in category entity in the ENTITY category. This item may be a site dependent bar code. This item is the unique identifier for the step whose product has been characterised. This category contains details for the chromatographic steps used in the purification of the protein. The temperature in degrees celsius at which this column was run. The type of column used in this step. The volume of the column used in this step. The date of production step. 2003-12-25 2003-12-25:09:00 This item is a pointer to pdbx_buffer.id in the PDBX_BUFFER category. The referenced buffer is that with which the protein was eluted. Details of the elution protocol. This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category. The referenced sequence is expected to be the amino acid sequence of the expressed product after the chromatography step. This item is a pointer to pdbx_buffer.id in the PDBX_BUFFER category. The referenced buffer is that in which the column was equilibrated. The rate at which the equilibration buffer flowed through the column. This item unique identifier for the next production step. This allows a workflow to have multiple entry points leading to a single product. Details of any post-chromatographic treatment of the protein sample. This data item is a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category. The method used to determine the concentration of the protein solution put onto the column. The concentration of the protein solution put onto the column. Details of the sample preparation prior to running the column. The volume of protein solution run on the column. The total volume of all the fractions pooled to give the purified protein solution. The method used to determine the yield The yield in milligrams of protein recovered in the pooled fractions. The value of attribute entry_id in category pdbx_entity_src_gen_chrom uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to attribute id in category entry. This item may be a site dependent bar code. The value of attribute entity_id in category pdbx_entity_src_gen_chrom uniquely identifies each protein contained in the project target complex proteins whose structure is to be determined. This data item is a pointer to attribute id in category entity in the ENTITY category. This item may be a site dependent bar code. This item is the unique identifier for this chromatography step. This category contains details for the cloning steps used in the overall protein production process. Each row in PDBX_ENTITY_SRC_GEN_CLONE should have an equivalent row in either PDBX_ENTITY_SRC_GEN_CLONE_LIGATION or PDBX_ENTITY_SRC_GEN_CLONE_RECOMBINATION. If only summary information is provided data in the later two categories may be omitted. The date of this production step. 2003-12-25 2003-12-25:09:00 This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category. The referenced nucleic acid sequence is that of the cloned product. The method used to insert the gene into the vector. For 'Ligation', an PDBX_ENTITY_SRC_GEN_CLONE_LIGATION entry with matching .step_id is expected. For 'Recombination', an PDBX_ENTITY_SRC_GEN_CLONE_RECOMBINATION entry with matching .step_id is expected. The type of marker included to allow selection of transformed cells This item unique identifier for the next production step. This allows a workflow to have multiple entry points leading to a single product. Details of any purification of the product. This data item is a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category. Summary of ligation or recombionation cloning used, the associated verification method and any purification of the product. The method used to transform the expression cell line with the vector Details of any modifications made to the named vector. The name of the vector used in this cloning step. The method used to verify that the incorporated gene is correct The value of attribute entry_id in category pdbx_entity_src_gen_clone uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to attribute id in category entry. This item may be a site dependent bar code. The value of attribute entity_id in category pdbx_entity_src_gen_clone uniquely identifies each protein contained in the project target protein complex whose structure is to be determined. This data item is a pointer to attribute id in category entity in the ENTITY category. This item may be a site dependent bar code. This item is the unique identifier for this cloning step. This category contains details for the ligation-based cloning steps used in the overall protein production process. attribute clone_step_id in category pdbx_entity_src_gen_clone_ligation in this category must point at a defined attribute step_id in category pdbx_entity_src_gen_clone. The details in PDBX_ENTITY_SRC_GEN_CLONE_LIGATION extend the details in PDBX_ENTITY_SRC_GEN_CLONE to cover ligation dependent cloning steps. The names of the enzymes used to cleave the vector. In addition an enzyme used to blunt the cut ends, etc., should be named here. Any details to be associated with this ligation step, e.g. the protocol. The names of the enzymes used to ligate the gene into the cleaved vector. The temperature at which the ligation experiment was performed, in degrees celsius. The duration of the ligation reaction in minutes. This item is a pointer to attribute entry_id in category pdbx_entity_src_gen_clone in the PDBX_ENTITY_SRC_GEN_CLONE category. This item is a pointer to attribute entity_id in category pdbx_entity_src_gen_clone in the PDBX_ENTITY_SRC_GEN_CLONE category. This item is a pointer to attribute step_id in category pdbx_entity_src_gen_clone in the PDBX_ENTITY_SRC_GEN_CLONE category. This category contains details for the recombination-based cloning steps used in the overall protein production process. It is assumed that these reactions will use commercially available kits. attribute clone_step_id in category pdbx_entity_src_gen_clone_recombination in this category must point at a defined attribute step_id in category pdbx_entity_src_gen_clone. The details in PDBX_ENTITY_SRC_GEN_CLONE_RECOMBINATION extend the details in PDBX_ENTITY_SRC_GEN_CLONE to cover recombination dependent cloning steps. Any details to be associated with this recombination step, e.g. the protocol or differences from the manufacturer's specified protocol. The names of the enzymes used for this recombination step. The name of the recombination system. This item is a pointer to attribute entry_id in category pdbx_entity_src_gen_clone in the PDBX_ENTITY_SRC_GEN_CLONE category. This item is a pointer to attribute entity_id in category pdbx_entity_src_gen_clone in the PDBX_ENTITY_SRC_GEN_CLONE category. This item is a pointer to attribute step_id in category pdbx_entity_src_gen_clone in the PDBX_ENTITY_SRC_GEN_CLONE category. This category contains details for the EXPRESSION steps used in the overall protein production process. It is hoped that this category will cover all forms of cell-based expression by reading induction as induction/transformation/transfection. Any C-terminal sequence tag as a string of one letter amino acid codes Any N-terminal sequence tag as a string of one letter amino acid codes. Any additives to the base media in which the expression host was grown. The name of the base media in which the expression host was grown. The temperature in degrees celsius at which the expression host was allowed to grow prior to induction/transformation/transfection. The time in hours for which the expression host was allowed to grow prior to induction/transformation/transfection. The volume of media in milliliters in which the expression host was grown. The date of production step. 2003-12-25 2003-12-25:09:00 This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category. The referenced sequence is expected to be the amino acid sequence of the expressed product. Details of the harvesting protocol. A specific line of cells used as the expression system The common name of the organism that served as host for the expression system. Where attribute host_org_tax_id in category pdbx_entity_src_gen_express is populated it is expected that this item may be derived by look up against the taxonomy database. Culture collection of the expression system A description of special aspects of the organism that served as host for the expression system. The scientific name of the organism that served as host for the expression system. It is expected that either this item or attribute host_org_tax_id in category pdbx_entity_src_gen_express should be populated. The strain of the organism that served as host for the expression system. Where attribute host_org_tax_id in category pdbx_entity_src_gen_express is populated it is expected that this item may be derived by a look up against the taxonomy database. The id for the NCBI taxonomy node corresponding to the organism that served as host for the expression system. The specific tissue which expressed the molecule. The vairant of the organism that served as host for the expression system. Where attribute host_org_tax_id in category pdbx_entity_src_gen_express is populated it is expected that this item may be derived by a look up against the taxonomy database. The chemical name of the inducing agent. Concentration of the inducing agent. Details of induction/transformation/transfection. The temperature in celsius at which the induced/transformed/transfected cells were grown. The time in hours after induction/transformation/transfection at which the optical density of the culture was measured. The multiplicity of infection for genes introduced by transfection, eg. for baculovirus-based expression. This item unique identifier for the next production step. This allows a workflow to have multiple entry points leading to a single product. This item is a pointer to attribute id in category pdbx_construct in the PDBX_CONSTRUCT category. The referenced entry will contain the nucleotide sequence that is to be expressed, including tags. The nature of the promoter controlling expression of the gene. T7 LacZ This data item is a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category. Details of how the harvested culture was stored. Summary of the details of the expression steps used in protein production. Identifies the type of vector used (plasmid, virus, or cosmid) in the expression system. The value of attribute entry_id in category pdbx_entity_src_gen_express uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to attribute id in category entry. This item may be a site dependent bar code. The value of attribute entity_id in category pdbx_entity_src_gen_express uniquely identifies each protein contained in the project target complex proteins whose structure is to be determined. This data item is a pointer to attribute id in category entity in the ENTITY category. This item may be a site dependent bar code. This item is the unique identifier for this expression step. This category contains details for OD time series used to monitor a given EXPRESSION step used in the overall protein production process. The optical density of the expression culture in arbitrary units at the timepoint specified. The time in hours after induction/transformation/transfection at which the optical density of the culture was measured. The value of attribute entry_id in category pdbx_entity_src_gen_express_timepoint is a pointer to attribute entry_id in category pdbx_entity_src_gen_express The value of attribute entity_id in category pdbx_entity_src_gen_express_timepoint is a pointer to attribute entity_id in category pdbx_entity_src_gen_express This item is a pointer to attribute step_id in category pdbx_entity_src_gen_express This items uniquely defines a timepoint within a series. This category contains details for the fraction steps used in the overall protein production process. Examples of fractionation steps are centrifugation and magnetic bead pull-down purification. The date of this production step. 2003-12-25 2003-12-25:09:00 String value containing details of the fractionation. This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category. The referenced sequence is expected to be the amino acid sequence of the expressed product after the fractionation step. This item describes the method of fractionation. This item unique identifier for the next production step. This allows a workflow to have multiple entry points leading to a single product. The fraction containing the protein of interest. The volume of the fraction containing the protein. The yield in milligrams of protein from the fractionation. The method used to determine the yield This data item is a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category. The temperature in degrees celsius at which the fractionation was performed. The value of attribute entry_id in category pdbx_entity_src_gen_fract uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to attribute id in category entry. This item may be a site dependent bar code. The value of attribute entity_id in category pdbx_entity_src_gen_fract uniquely identifies each protein contained in the project target protein complex whose structure is to be determined. This data item is a pointer to attribute id in category entity in the ENTITY category. This item may be a site dependent bar code. This item is the unique identifier for this fractionation step. This category contains details for the cell lysis steps used in the overall protein production process. This item is a pointer to pdbx_buffer.id in the PDBX_BUFFER category. The referenced buffer is that in which the lysis was performed. The volume in milliliters of buffer in which the lysis was performed. The date of this production step. 2003-12-25 2003-12-25:09:00 String value containing details of the lysis protocol. This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category. The referenced sequence is expected to be the amino acid sequence of the expressed product after lysis. The lysis method. This item unique identifier for the next production step. This allows a workflow to have multiple entry points leading to a single product. This data item is a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category. The temperature in degrees celsius at which the lysis was performed. The time in seconds of the lysis experiment. The value of attribute entry_id in category pdbx_entity_src_gen_lysis uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to attribute id in category entry. This item may be a site dependent bar code. The value of attribute entity_id in category pdbx_entity_src_gen_lysis uniquely identifies each protein contained in the project target protein complex whose structure is to be determined. This data item is a pointer to attribute id in category entity in the ENTITY category. This item may be a site dependent bar code. This item is the unique identifier for this lysis step. This category contains details for the DIGEST steps used in the overall protein production process. The digestion is assumed to be applied to the result of the previous production step, or the gene source if this is the first production step. Example 1 - hypothetical example <PDBx:pdbx_entity_src_gen_prod_digestCategory> <PDBx:pdbx_entity_src_gen_prod_digest entry_id="111000111" entity_id="222000111" step_id="2"> <PDBx:next_step_id>3</PDBx:next_step_id> <PDBx:end_construct_id>440050000123</PDBx:end_construct_id> <PDBx:robot_id>5</PDBx:robot_id> <PDBx:date>2002-07-12:15:13</PDBx:date> <PDBx:restriction_enzyme_1>NcoI</PDBx:restriction_enzyme_1> <PDBx:restriction_enzyme_2>BamII</PDBx:restriction_enzyme_2> <PDBx:purification_details> No purification</PDBx:purification_details> </PDBx:pdbx_entity_src_gen_prod_digest> </PDBx:pdbx_entity_src_gen_prod_digestCategory> The date of this production step. 2003-12-25 This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category. The referenced nucleic acid sequence is that of the digest product This item unique identifier for the next production step. This allows a workflow to have multiple entry points leading to a single product. String value containing details of any purification of the product of the digestion. The first enzyme used in the restriction digestion. The sites at which this cuts can be derived from the sequence. BamIII The second enzyme used in the restriction digestion. The sites at which this cuts can be derived from the sequence. This data item is a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category. Summary of the details of restriction digestion any purification of the product of the digestion. The value of attribute entry_id in category pdbx_entity_src_gen_prod_digest uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to attribute id in category entry. This item may be a site dependent bar code. The value of attribute entity_id in category pdbx_entity_src_gen_prod_digest uniquely identifies each protein contained in the project target protein complex whose structure is to be determined. This data item is a pointer to attribute id in category entity in the ENTITY category. This item may be a site dependent bar code. This item is the unique identifier for this digestion step. This category contains details for process steps that are not explicitly catered for elsewhere. It provides some basic details as well as placeholders for a list of parameters and values (the category PDBX_ENTITY_SRC_GEN_PROD_OTHER_PARAMETER). Note that processes that have been modelled explicitly should not be represented using this category. The date of this process step. 2003-12-25 2003-12-25:09:00 Additional details of this process step. This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category. The referenced nucleic acid sequence is that of the product of the process step. This item unique identifier for the next production step. This allows a workflow to have multiple entry points leading to a single product. Name of this process step. This data item is a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category. The referenced robot is the robot responsible for the process step The value of attribute entry_id in category pdbx_entity_src_gen_prod_other uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to attribute id in category entry. This item may be a site dependent bar code. The value of attribute entity_id in category pdbx_entity_src_gen_prod_other uniquely identifies each protein contained in the project target protein complex whose structure is to be determined. This data item is a pointer to attribute id in category entity in the ENTITY category. This item may be a site dependent bar code. This item is the unique identifier for this process step. This category contains parameters and values required to capture information about a particular process step Additional details about the parameter The value of the parameter The value of attribute entry_id in category pdbx_entity_src_gen_prod_other_parameter is a pointer to attribute entry.id in category pdbx_entity_src_gen_prod_other The value of attribute entity_id in category pdbx_entity_src_gen_prod_other_parameter is a pointer to attribute entity_id in category pdbx_entity_src_gen_prod_other This item is a pointer to attribute step_id in category pdbx_entity_src_gen_prod_other The name of the parameter associated with the process step This category contains details for the PCR steps used in the overall protein production process. The PCR is assumed to be applied to the result of the previous production step, or the gene source if this is the first production step. Example 1 - hypothetical example <PDBx:pdbx_entity_src_gen_prod_pcrCategory> <PDBx:pdbx_entity_src_gen_prod_pcr entry_id="111000111" entity_id="222000111" step_id="1"> <PDBx:next_step_id>2</PDBx:next_step_id> <PDBx:end_construct_id>440050000111</PDBx:end_construct_id> <PDBx:robot_id>5</PDBx:robot_id> <PDBx:date>2002-07-12:15:13</PDBx:date> <PDBx:forward_primer_id>2</PDBx:forward_primer_id> <PDBx:reverse_primer_id>3</PDBx:reverse_primer_id> <PDBx:reaction_details> Annealing temperature = 70 C Annealing time = 60 s Extending temperature = 74 C Extending time = 120 s Melting temperature = 95 C Melting time = 120 s Number of cycles = 40 Polymerase = KOD Template = 10 pmol Primer = 25 pmol Total volume = 25 ul</PDBx:reaction_details> <PDBx:purification_details> No purification</PDBx:purification_details> </PDBx:pdbx_entity_src_gen_prod_pcr> </PDBx:pdbx_entity_src_gen_prod_pcrCategory> The date of this production step. 2003-12-25 2003-12-25:09:00 This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category. The referenced nucleic acid sequence is that of the PCR product. This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category. The referenced nucleic acid sequence is that of the forward primer. This item unique identifier for the next production step. This allows a workflow to have multiple entry points leading to a single product. String value containing details of any purification of the product of the PCR reaction. String value containing details of the PCR reaction. This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category. The referenced nucleic acid sequence is that of the reverse primer. This data item is a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category. The referenced robot is the robot responsible for the PCR reaction (normally the heat cycler). Summary of the details of the PCR reaction any purification of the product of the PCR reaction. The value of attribute entry_id in category pdbx_entity_src_gen_prod_pcr uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to attribute id in category entry. This item may be a site dependent bar code. The value of attribute entity_id in category pdbx_entity_src_gen_prod_pcr uniquely identifies each protein contained in the project target protein complex whose structure is to be determined. This data item is a pointer to attribute id in category entity in the ENTITY category. This item may be a site dependent bar code. This item is the unique identifier for this PCR step. This category contains details for the protein purification tag removal steps used in the overall protein production process This item is a pointer to pdbx_buffer.id in the PDBX_BUFFER category. The referenced buffer is that in which the cleavage was performed. The temperature in degrees celsius at which the cleavage was performed. The time in minutes for the cleavage reaction The date of production step. 2003-12-25 2003-12-25:09:00 Details of this tag removal step. This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category. The referenced sequence is expected to be the amino acid sequence of the expressed product after the proteolysis step. This item unique identifier for the next production step. This allows a workflow to have multiple entry points leading to a single product. The name of the protease used for cleavage. The ratio of protein to protease used for the cleavage. = mol protein / mol protease This data item is a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category. The value of attribute entry_id in category pdbx_entity_src_gen_proteolysis uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to attribute id in category entry. This item may be a site dependent bar code. The value of attribute entity_id in category pdbx_entity_src_gen_proteolysis uniquely identifies each protein contained in the project target complex proteins whose structure is to be determined. This data item is a pointer to attribute id in category entity in the ENTITY category. This item may be a site dependent bar code. This item is the unique identifier for this tag removal step. This category contains details for the final purified protein product. Note that this category does not contain the amino acid sequence of the protein. The sequence will be found in the ENTITY_POLY_SEQ entry with matching entity_id. Only one PDBX_ENTITY_SRC_GEN_PURE category is allowed per entity, hence there is no step_id for this category. The method used to measure the protein concentration Details of the protein concentration procedure This data item is a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category. The date of production step. 2003-12-25 2003-12-25:09:00 When present, this item should be a globally unique identifier that identifies the final product. It is envisaged that this should be the same as and product code associated with the sample and would provide the key by which information about the production process may be extracted from the protein production facility. For files describing the protein production process (i.e. where attribute type in category entity is 'P' or 'E') this should have the same value as attribute id in category entry The final concentration of the protein. The oligomeric state of the protein. Monomeric is 1, dimeric 2, etc. The purity of the protein (percent). The yield of protein in milligrams. This item is a pointer to pdbx_buffer.id in the PDBX_BUFFER category. The referenced buffer is that in which the protein was stored. The temperature in degrees celsius at which the protein was stored. Summary of the details of protein purification method used to obtain the final protein product. This description should include any lysis, fractionation, proteolysis, refolding, chromatography used as well as the method used the characterize the final product. The value of attribute entry_id in category pdbx_entity_src_gen_pure uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to attribute id in category entry. This item may be a site dependent bar code. The value of attribute entity_id in category pdbx_entity_src_gen_pure uniquely identifies each protein contained in the project target complex proteins whose structure is to be determined. This data item is a pointer to attribute id in category entity in the ENTITY category. This item may be a site dependent bar code. This item unique identifier the production step. This category contains details for the refolding steps used in the overall protein production process. The date of this production step. 2003-12-25 2003-12-25:09:00 This item is a pointer to pdbx_buffer.id in the PDBX_BUFFER category. The referenced buffer is that in which the protein was denatured. String value containing details of the refolding. This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category. The referenced sequence is expected to be the amino acid sequence of the expressed product after the refolding step. This item unique identifier for the next production step. This allows a workflow to have multiple entry points leading to a single product. This item is a pointer to pdbx_buffer.id in the PDBX_BUFFER category. The referenced buffer is that in which the protein was refolded. This data item is a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category. This item is a pointer to pdbx_buffer.id in the PDBX_BUFFER category. The referenced buffer is that in which the refolded protein was stored. The temperature in degrees celsius at which the protein was refolded. The time in hours over which the protein was refolded. The value of attribute entry_id in category pdbx_entity_src_gen_refold uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to attribute id in category entry. This item may be a site dependent bar code. The value of attribute entity_id in category pdbx_entity_src_gen_refold uniquely identifies each protein contained in the project target protein complex whose structure is to be determined. This data item is a pointer to attribute id in category entity in the ENTITY category. This item may be a site dependent bar code. This item is the unique identifier for this refolding step. PDBX_ENTITY_SRC_SYN records the details about each chemically synthesized molecule (entity) in the asymmetric unit. A description of special aspects of the source for the synthetic entity. This sequence occurs naturally in humans. This data item is a pointer to attribute id in category entity in the ENTITY category. 1 2 3 4 This section provides a tabulation of constraint data. This example uses the data from the MCP-1 structure determination. Remember this is a dimer so there are intersubunit constraints as well as intrasubunit constraints. <PDBx:pdbx_nmr_constraintsCategory> <PDBx:pdbx_nmr_constraints entry_id="1ABC"> <PDBx:NOE_constraints_total>4458</PDBx:NOE_constraints_total> <PDBx:NOE_intraresidue_total_count>1144</PDBx:NOE_intraresidue_total_count> <PDBx:NOE_sequential_total_count>272</PDBx:NOE_sequential_total_count> <PDBx:NOE_medium_range_total_count>1004</PDBx:NOE_medium_range_total_count> <PDBx:NOE_long_range_total_count>1356</PDBx:NOE_long_range_total_count> <PDBx:protein_phi_angle_constraints_total_count>96</PDBx:protein_phi_angle_constraints_total_count> </PDBx:pdbx_nmr_constraints> </PDBx:pdbx_nmr_constraintsCategory> The total number of nucleic acid alpha-angle constraints used in the final structure calculation. 18 The total number of nucleic acid beta-angle constraints used in the final structure calculation. 24 The total number of nucleic acid chi-angle constraints used in the final structure calculation. 15 The total number of nucleic acid delta-angle constraints used in the final structure calculation. 15 The total number of nucleic acid epsilon-angle constraints used in the final structure calculation. 31 The total number of nucleic acid gamma-angle constraints used in the final structure calculation. 12 The total number of nucleic acid other-angle constraints used in the final structure calculation. 5 The total number of nucleic acid sugar pucker constraints used in the final structure calculation. 10 The total number of all NOE constraints used in the final structure calculation. 4458 The total number of interentity, NOE constraints used in the final structure calculation. This field should only be if system is complex -i.e more than one entity e.g. a dimer or ligand-protein complex 272 Describe the method used to quantify the NOE and ROE values. NOE buildup curves with 50, 75, 150 ms mixing times were analyzed. Noesy cross peak intensities were classified into three different catagories with distances of 1.8-2.7 A, 1.8-3.5 A, 1.8- 5.0 A for strong, medium and weak NOEs. The total number of all intraresidue, [i-j]=0, NOE constraints used in the final structure calculation. 1144 The total number of long range [i-j]>5 NOE constraints used in the final structure calculation. 1356 The total number of medium range 1<[i-j]<=5 NOE constraints used in the final structure calculation. 682 Describe any corrections that were made to the NOE data for motional averaging. Replace with item example text Describe any corrections made for pseudoatoms Pseudo-atoms nomenclature and corrections according to Wuethrich, Billeter, and Braun, J. Mol.Biol.(1983) 169, 949-961. Pseudoatoms were not used. The total number of sequential, [i-j]=1, NOE constraints used in the final structure calculation. 1004 The total number of disulfide bond constraints used in the final structure calculation. 3 The total number of hydrogen bond constraints used in the final structure calculation. 6 The total number of chi angle constraints used in the final structure calculation. 66 The total number of other angle constraints used in the final structure calculation. 0 The total number of phi angle constraints used in the final structure calculation 96 The total number of psi angle constraints used in the final structure calculation. 0 You can leave this blank as an ID will be assigned by the MSD to the constraint file. Experimental details of the NMR study that have not been described elsewhere in this deposition. Additional details describing the NMR experiment. This structure was determined using standard 2D homonuclear techniques. The structure was determined using triple-resonance NMR spectroscopy. The entry ID for the structure determination. This category contains the information that describes the ensemble of deposited structures. If only an average structure has been deposited skip this section. This example uses the data from the MCP-1 study. <PDBx:pdbx_nmr_ensembleCategory> <PDBx:pdbx_nmr_ensemble entry_id="1ABC"> <PDBx:conformers_calculated_total_number>40</PDBx:conformers_calculated_total_number> <PDBx:conformers_submitted_total_number>20</PDBx:conformers_submitted_total_number> <PDBx:conformer_selection_criteria>structures with the least restraint violations</PDBx:conformer_selection_criteria> <PDBx:representative_conformer>1</PDBx:representative_conformer> </PDBx:pdbx_nmr_ensemble> </PDBx:pdbx_nmr_ensembleCategory> The average number of constraint violations on a per residue basis for the ensemble. 0.25 The average number of constraints per residue for the ensemble 30.2 The average distance restraint violation for the ensemble. 0.11 The average torsion angle constraint violation for the ensemble. 2.4 By highlighting the appropriate choice(s), describe how the submitted conformer (models) were selected. structures with the lowest energy structures with the least restraint violations structures with acceptable covalent geometry structures with favorable non-bond energy target function back calculated data agree with experimental NOESY spectrum all calculated structures submitted The submitted conformer models are the 25 structures with the lowest energy. The submitted conformer models are those with the fewest number of constraint violations. The total number of conformer (models) that were calculated in the final round. 40 The number of conformer (models) that are submitted for the ensemble. 20 Describe the method used to calculate the distance constraint violation statistics, i.e. are they calculated over all the distance constraints or calculated for violations only? Statistics were calculated over all of the distance constraints. Statistics were calculated for violations only The maximum distance constraint violation for the ensemble. 0.4 The maximum lower distance constraint violation for the ensemble. 0.3 The maximum torsion angle constraint violation for the ensemble. 4 The maximum upper distance constraint violation for the ensemble. 0.4 The number of the conformer identified as most representative. 20 This item describes the method used to calculate the torsion angle constraint violation statistics. i.e. are the entered values based on all torsion angle or calculated for violations only? Statistics were calculated over all the torsion angle constraints. Statistics were calculated for torsion angle constraints violations only. Leave this blank as the ID is provided by the MSD Structural statistics are derived from molecular dynamics and simulated annealing programs. This example is derived from the MCP-1 structure calculation statistics. For this structure the statistics were calculated over residues 5-69 for both the monomer and dimer . <PDBx:pdbx_nmr_ensemble_rmsCategory> <PDBx:pdbx_nmr_ensemble_rms entry_id="1ABC"> <PDBx:residue_range_begin>5</PDBx:residue_range_begin> <PDBx:chain_range_begin>A</PDBx:chain_range_begin> <PDBx:residue_range_end>69</PDBx:residue_range_end> <PDBx:chain_range_end>A</PDBx:chain_range_end> <PDBx:atom_type>all heavy atoms</PDBx:atom_type> <PDBx:distance_rms_dev>0.22</PDBx:distance_rms_dev> <PDBx:distance_rms_dev_error>0.06</PDBx:distance_rms_dev_error> </PDBx:pdbx_nmr_ensemble_rms> </PDBx:pdbx_nmr_ensemble_rmsCategory> Statistics are often calculated over only some of the atoms, e.g. backbone, or heavy atoms. Describe which type of atoms are used for the statistical analysis. backbone atoms heavy atoms The bond angle rmsd to the target values for the ensemble. 0.60 The error in the bond angle rmsd. 0.01 The beginning chain id. A The ending chain id: A Describe the method for calculating the coordinate average rmsd. Replace with item example text The covalent bond rmsd to the target value for the ensemble. 0.0066 The error in the covalent bond rmsd. 0.0001 The dihedral angle rmsd to the target values for the ensemble. 0.66 The error of the rmsd dihedral angles. 0.07 The distance rmsd to the mean structure for the ensemble of structures. 0.22 The error in the distance rmsd. 0.07 The improper torsion angle rmsd to the target values for the ensemble. 0.64 The error in the improper torsion angle rmsd. 0.04 The peptide planarity rmsd. 0.11 The error in the peptide planarity rmsd. 0.05 Structure statistics are often calculated only over the well-ordered region(s) of the biopolymer. Portions of the macromolecule are often mobile and disordered, hence they are excluded in calculating the statistics. To define the range(s) over which the statistics are calculated, enter the beginning residue number(s): e.g. if the regions used were 5-32 and 41-69, enter 5,41 5 41 The ending residue number: e.g. 32,69. 32 69 '?' In this section, enter information on those experiments that were used to generate constraint data. For each NMR experiment indicate which sample and which sample conditions were used for the experiment. This example was taken from the MCP-1 study. <PDBx:pdbx_nmr_exptlCategory> <PDBx:pdbx_nmr_exptl experiment_id="1" solution_id="3" conditions_id="1"> <PDBx:type>3D_15N-separated_NOESY</PDBx:type> </PDBx:pdbx_nmr_exptl> <PDBx:pdbx_nmr_exptl experiment_id="2" solution_id="1" conditions_id="1"> <PDBx:type>3D_13C-separated_NOESY</PDBx:type> </PDBx:pdbx_nmr_exptl> <PDBx:pdbx_nmr_exptl experiment_id="3" solution_id="1" conditions_id="2"> <PDBx:type>4D_13C/15N-separated_NOESY</PDBx:type> </PDBx:pdbx_nmr_exptl> <PDBx:pdbx_nmr_exptl experiment_id="4" solution_id="1" conditions_id="1"> <PDBx:type>4D_13C-separated_NOESY</PDBx:type> </PDBx:pdbx_nmr_exptl> <PDBx:pdbx_nmr_exptl experiment_id="5" solution_id="1" conditions_id="1"> <PDBx:type>3D_15N-separated_ROESY</PDBx:type> </PDBx:pdbx_nmr_exptl> <PDBx:pdbx_nmr_exptl experiment_id="6" solution_id="3" conditions_id="1"> <PDBx:type>3D_13C-separated_ROESY</PDBx:type> </PDBx:pdbx_nmr_exptl> </PDBx:pdbx_nmr_exptlCategory> The type of NMR experiment. 2D NOESY 3D_15N-separated_NOESY 3D_13C-separated_NOESY 4D_13C-separated_NOESY 4D_13C/15N-separated_NOESY 3D_15N-separated_ROESY 3D_13C-separated_ROESY HNCA-J HNHA DQF-COSY P-COSY PE-COSY E-COSY A numerical ID for each experiment. 1 2 3 The number to identify the set of sample conditions. 1 2 3 The solution_id from the Experimental Sample to identify the sample that these conditions refer to. [Remember to save the entries here before returning to the Experimental Sample form] 1 2 3 The chemical constituents of each NMR sample. Each sample is identified by a number and each component in the sample is identified by name. Example 1 This example was taken from the study of MCP-1 which is a dimer under the conditions studied. Three solutions with different isotope compositions were studied. <PDBx:pdbx_nmr_exptl_sampleCategory> <PDBx:pdbx_nmr_exptl_sample solution_id="1" component="MCP-1"> <PDBx:concentration>2</PDBx:concentration> <PDBx:concentration_units>mM</PDBx:concentration_units> <PDBx:isotopic_labeling>U-15N,13C</PDBx:isotopic_labeling> </PDBx:pdbx_nmr_exptl_sample> <PDBx:pdbx_nmr_exptl_sample solution_id="1" component="H2O"> <PDBx:concentration>90</PDBx:concentration> <PDBx:concentration_units>&#37;</PDBx:concentration_units> </PDBx:pdbx_nmr_exptl_sample> <PDBx:pdbx_nmr_exptl_sample solution_id="1" component="D2O"> <PDBx:concentration>10</PDBx:concentration> <PDBx:concentration_units>&#37;</PDBx:concentration_units> </PDBx:pdbx_nmr_exptl_sample> </PDBx:pdbx_nmr_exptl_sampleCategory> Example 2 This example was taken from the study of MCP-1 which is a dimer under the conditions studied. Three solutions with different isotope compositions were studied. <PDBx:pdbx_nmr_exptl_sampleCategory> <PDBx:pdbx_nmr_exptl_sample solution_id="2" component="MCP-1"> <PDBx:concentration>1</PDBx:concentration> <PDBx:concentration_units>mM</PDBx:concentration_units> <PDBx:isotopic_labeling>U-50&#37; 15N</PDBx:isotopic_labeling> </PDBx:pdbx_nmr_exptl_sample> <PDBx:pdbx_nmr_exptl_sample solution_id="2" component="H2O"> <PDBx:concentration>90</PDBx:concentration> <PDBx:concentration_units>&#37;</PDBx:concentration_units> </PDBx:pdbx_nmr_exptl_sample> <PDBx:pdbx_nmr_exptl_sample solution_id="2" component="D2O"> <PDBx:concentration>10</PDBx:concentration> <PDBx:concentration_units>&#37;</PDBx:concentration_units> </PDBx:pdbx_nmr_exptl_sample> </PDBx:pdbx_nmr_exptl_sampleCategory> The concentration value of the component. 2.0 2.7 0.01 The concentration units of the component. mg/mL for mg per milliliter mM for millimolar % for percent by volume The isotopic composition of each component, including the % labeling level, if known. For example: 1. Uniform (random) labeling with 15N: U-15N 2. Uniform (random) labeling with 13C, 15N at known labeling levels: U-95% 13C;U-98% 15N 3. Residue selective labeling: U-95% 15N-Thymine 4. Site specific labeling: 95% 13C-Ala18, 5. Natural abundance labeling in an otherwise uniformly labled biomolecule is designated by NA: U-13C; NA-K,H U-13C,15N U-2H The name (number) of the sample. 1 2 3 The name of each component in the sample ribonuclease DNA strand 1 TRIS buffer sodium chloride H2O D2O The experimental conditions used to for each sample. Each set of conditions is identified by a numerical code. This example was taken from a pH stability study. <PDBx:pdbx_nmr_exptl_sample_conditionsCategory> <PDBx:pdbx_nmr_exptl_sample_conditions conditions_id="1"> <PDBx:temperature>298</PDBx:temperature> <PDBx:pressure>ambient</PDBx:pressure> <PDBx:pH>7</PDBx:pH> <PDBx:ionic_strength>25mM NaCl</PDBx:ionic_strength> </PDBx:pdbx_nmr_exptl_sample_conditions> <PDBx:pdbx_nmr_exptl_sample_conditions conditions_id="2"> <PDBx:temperature>298</PDBx:temperature> <PDBx:pressure>ambient</PDBx:pressure> <PDBx:pH>3</PDBx:pH> <PDBx:ionic_strength>25mM NaCl</PDBx:ionic_strength> </PDBx:pdbx_nmr_exptl_sample_conditions> </PDBx:pdbx_nmr_exptl_sample_conditionsCategory> The ionic strength at which the NMR data were collected -in lieu of this enter the concentration and identity of the salt in the sample. The pH at which the NMR data were collected. 3.1 7.0 The pressure at which NMR data were collected. ambient 1atm The units of pressure at which NMR data were collected. Pa atm Torr The temperature (in Kelvin) at which NMR data were collected. 298 The condition number as defined above. 1 2 3 The final force constants, including units, employed for the various experimental constraints, covalent geometry constraints, and the non-bonded interaction terms in the target function used for simulated annealing. This example is taken from a study of BAF, a dimeric DNA binding protein. The final force constants in the target function used for simulated annealing are: Experimental Constraint terms: Distance (NOE,H-bonds), Torsion angles, J coupling, 13C shifts, 1H shifts, Dipolar coupling, D isotope shifts Covalent Geometry Constraint terms: Bond lengths, Angles, Impropers Non-bonded Interaction terms: van der Waals, Type of van der Waals term, Conformational database potential, Radius of gyration. <PDBx:pdbx_nmr_force_constantsCategory> <PDBx:pdbx_nmr_force_constants entry_id="1ABC"> <PDBx:exptl_distance_term>30.</PDBx:exptl_distance_term> <PDBx:exptl_distance_term_units>kcal/mol/A**2</PDBx:exptl_distance_term_units> <PDBx:exptl_torsion_angles_term>200.</PDBx:exptl_torsion_angles_term> <PDBx:exptl_torsion_angles_term_units>kcal/mol/rad**2</PDBx:exptl_torsion_angles_term_units> <PDBx:exptl_J_coupling_term>1.</PDBx:exptl_J_coupling_term> <PDBx:exptl_J_coupling_term_units>kcal/mol/Hz**2</PDBx:exptl_J_coupling_term_units> <PDBx:exptl_13C_shift_term>0.5</PDBx:exptl_13C_shift_term> <PDBx:exptl_13C_shift_term_units>kcal/mol/ppm**2</PDBx:exptl_13C_shift_term_units> <PDBx:exptl_1H_shift_term>7.5</PDBx:exptl_1H_shift_term> <PDBx:exptl_1H_shift_term_units>kcal/mol/ppm**2</PDBx:exptl_1H_shift_term_units> <PDBx:covalent_geom_bond_term>1000.</PDBx:covalent_geom_bond_term> <PDBx:covalent_geom_bond_term_units>kcal/mol/A**2</PDBx:covalent_geom_bond_term_units> <PDBx:non-bonded_inter_van_der_Waals_term_type>4.</PDBx:non-bonded_inter_van_der_Waals_term_type> </PDBx:pdbx_nmr_force_constants> </PDBx:pdbx_nmr_force_constantsCategory> The final force constant for covalent geometry angle constraints term employed in the target function used for simulated annealing. 500 The units for the force constant for the covalent geometry angle constraints term. kcal/mol/rad**2 The final force constant for the covalent geometry bond length constraints term employed in the target function used for simulated annealing. 1000 The units for the force constant for the covalent geometry bond length constraints term. kcal/mol/A**2 The final force constant for covalent geometry impropers contstraints term employed in the target function used for simulated annealing. 500 The units for the force constant for the covalent geometry impropers constraints term. kcal/mol/rad**2 The final force constant for 13C shift constraints term employed in the target function used for simulated annealing. 0.5 The units for the force constant for the 13C shift constraints term. kcal/mol/ppm**2 The final force constant for 1H shift constraints term employed in the target function used for simulated annealing. 7.5 The units for the force constant for the 1H shift constraints term. kcal/mol/ppm**2 The final force constant for Deuterium isotope shift constraints term employed in the target function used for simulated annealing. 0.5 The units for the force constant for the Deuterium isotope shift constraints term. kcal/mol/ppb**2 The final force constant for J coupling term employed in the target function used for simulated annealing. 1 The units for the force constant for the J coupling term. kcal/mol/Hz**2 The final force constant for dipolar coupling constraint term employed in the target function used for simulated annealing. 1 The units for the force constant for the dipolar coupling constraints term. kcal/mol/Hz**2 The final force constant for distance (NOEs) constraints term employed in the target function used for simulated annealing. 30 The units for the force constant for the distance constraints term. kcal/mol/ A**2 The final force constant for the torsion angle term employed in the target function used for simulated annealing. 200 The units for the force constant for the torsion angle constraints term. kcal/mol/rad**2 The force constant used for the non-bonded interaction conformational database potential term employed in the target function used for simulated annealing. 1.0 The force constant used for the non-bonded interaction radius of gyration term employed in the target function used for simulated annealing. 100 The units for the force constant for the radius of gyration term. kcal/mol/ A**2 The force constant used for the non-bonded interaction van der Waals term employed in the target function used for simulated annealing. 4 The type of van der Waals term employed in the target function used for simulated annealing. quartic The units for the force constant for the van der Waals term. kcal/mol/ A**4 You can leave this blank as an ID will be assigned by the RCSB. Describe the method and details of the refinement of the deposited structure. This example is drawn from the MCP-1 structure. <PDBx:pdbx_nmr_refineCategory> <PDBx:pdbx_nmr_refine entry_id="1ABC"> <PDBx:method>torsion angle dynamics</PDBx:method> </PDBx:pdbx_nmr_refine> </PDBx:pdbx_nmr_refineCategory> Additional details about the NMR refinement. Additional comments about the NMR refinement can be placed here, e.g. the structures are based on a total of 3344 restraints, 3167 are NOE-derived distance constraints, 68 dihedral angle restraints,109 distance restraints from hydrogen bonds. The method used to determine the structure. distance geometry simulated annealing molecular dynamics matrix relaxation torsion angle dynamics You can leave this blank as an ID will be assigned by the RCSB to the constraint file. An average structure is often calculated in addition to the ensemble, or one of the ensemble is selected as a representative structure. This section describes selection of the representative structure. This example is drawn from the MCP-1 structure. <PDBx:pdbx_nmr_representativeCategory> <PDBx:pdbx_nmr_representative entry_id="1ABC"> <PDBx:conformer_id>15</PDBx:conformer_id> <PDBx:selection_criteria>lowest energy</PDBx:selection_criteria> </PDBx:pdbx_nmr_representative> </PDBx:pdbx_nmr_representativeCategory> If a member of the ensemble has been selected as a representative structure, identify it by its model number. 15 By highlighting the appropriate choice(s), describe the criteria used to select this structure as a representative structure, or if an average structure has been calculated describe how this was done. The structure closest to the average. The structure with the lowest energy was selected. The structure with the fewest number of violations was selected. A minimized average structure was calculated. msd will assign the ID. Complete description of each NMR sample, including the solvent system used. This example was taken from the study of MCP-1 which is a dimer under the conditions studied. Three solutions with different isotope compositions were studied. <PDBx:pdbx_nmr_sample_detailsCategory> <PDBx:pdbx_nmr_sample_details solution_id="1"> <PDBx:solvent_system>MCP-1</PDBx:solvent_system> <PDBx:contents>2 mM U-15N,13C, H2O 90 &#37;, D2O 10 &#37;</PDBx:contents> </PDBx:pdbx_nmr_sample_details> <PDBx:pdbx_nmr_sample_details solution_id="2"> <PDBx:solvent_system>MCP-1</PDBx:solvent_system> <PDBx:contents>1 mM U-50&#37; 15N, MCP-1 1 mM U-50&#37; 13C, H2O 90 &#37;, D2O 10 &#37;</PDBx:contents> </PDBx:pdbx_nmr_sample_details> <PDBx:pdbx_nmr_sample_details solution_id="3"> <PDBx:solvent_system>MCP-1</PDBx:solvent_system> <PDBx:contents>2 mM U-15N, H2O 90 &#37;, D2O 10 &#37;</PDBx:contents> </PDBx:pdbx_nmr_sample_details> </PDBx:pdbx_nmr_sample_detailsCategory> A complete description of each NMR sample. Include the concentration and concentration units for each component (include buffers, etc.). For each component describe the isotopic composition, including the % labeling level, if known. For example: 1. Uniform (random) labeling with 15N: U-15N 2. Uniform (random) labeling with 13C, 15N at known labeling levels: U-95% 13C;U-98% 15N 3. Residue selective labeling: U-95% 15N-Thymine 4. Site specific labeling: 95% 13C-Ala18, 5. Natural abundance labeling in an otherwise uniformly labeled biomolecule is designated by NA: U-13C; NA-K,H 2mM Ribonuclease U-15N,13C; 50mM phosphate buffer NA; 90% H2O, 10% D2O The solvent system used for this sample. 90% H2O, 10% D2O The name (number) of the sample. 1 2 3 Description of the software that was used for data collection, data processing, data analysis, structure calculations and refinement. The description should include the name of the software, the author of the software and the version used. This example describes the software used in the MCP-1 study. <PDBx:pdbx_nmr_softwareCategory> <PDBx:pdbx_nmr_software name="UXNMR" version="940501.3" classification="collection"> <PDBx:authors>Bruker</PDBx:authors> </PDBx:pdbx_nmr_software> <PDBx:pdbx_nmr_software name="FELIX" version="1.1" classification="processing"> <PDBx:authors>Hare</PDBx:authors> </PDBx:pdbx_nmr_software> <PDBx:pdbx_nmr_software name="ANSIG" version="3.0" classification="data analysis"> <PDBx:authors>Kraulis</PDBx:authors> </PDBx:pdbx_nmr_software> <PDBx:pdbx_nmr_software name="X-PLOR" version="3.8" classification="structure calculation"> <PDBx:authors>Brunger</PDBx:authors> </PDBx:pdbx_nmr_software> <PDBx:pdbx_nmr_software name="X-PLOR" version="3.8" classification="refinement"> <PDBx:authors>Brunger</PDBx:authors> </PDBx:pdbx_nmr_software> </PDBx:pdbx_nmr_softwareCategory> The name of the authors of the software used in this procedure. Brunger Guentert The name of the software used for the task. ANSIG AURELIA AZARA CHARMM CORMA DIANA DYANA DSPACE DISGEO DGII DISMAN DINOSAUR DISCOVER FELIX FT_NMR GROMOS IRMA MARDIGRAS NMRPipe SA UXNMR VNMR X-PLOR XWINNMR The version of the software. 940501.3 2.1 The purpose of the software. collection processing data analysis structure solution refinement iterative matrix relaxation The details about each spectrometer used to collect data for this deposition. The instruments described here are the ones used for the MCP-1 studies. <PDBx:pdbx_nmr_spectrometerCategory> <PDBx:pdbx_nmr_spectrometer spectrometer_id="1"> <PDBx:type>Bruker AMX</PDBx:type> <PDBx:field_strength>600</PDBx:field_strength> </PDBx:pdbx_nmr_spectrometer> <PDBx:pdbx_nmr_spectrometer spectrometer_id="2"> <PDBx:type>Bruker AMX</PDBx:type> <PDBx:field_strength>500</PDBx:field_strength> </PDBx:pdbx_nmr_spectrometer> </PDBx:pdbx_nmr_spectrometerCategory> Select the field strength for protons in MHz. 360 400 500 600 750 800 850 900 950 1000 The name of the manufacturer of the spectrometer. Varian Bruker JEOL GE The model of the NMR spectrometer. AVANCE WH WM AM AMX DMX DRX MSL OMEGA OMEGA PSG GX GSX A AL EC EX LA ECP VXRS UNITY UNITYPLUS INOVA Select the instrument manufacturer(s) and the model(s) of the NMR(s) used for this work. Bruker WH Bruker WM Bruker AM Bruker AMX Bruker DMX Bruker DRX Bruker MSL Bruker AVANCE GE Omega GE Omega PSG JEOL GX JEOL GSX JEOL A JEOL AL JEOL EC JEOL EX JEOL LA JEOL ECP Varian VXRS Varian UNITY Varian UNITYplus Varian INOVA other Assign a numerical ID to each instrument. 1 2 3 The PDBX_NONPOLY_SCHEME category provides residue level nomenclature mapping for non-polymer entities. Example 1 - <PDBx:pdbx_nonpoly_schemeCategory> <PDBx:pdbx_nonpoly_scheme asym_id="C"> <PDBx:entity_id>3</PDBx:entity_id> <PDBx:mon_id>HOH</PDBx:mon_id> <PDBx:ndb_seq_num>100</PDBx:ndb_seq_num> <PDBx:pdb_seq_num>100</PDBx:pdb_seq_num> <PDBx:auth_seq_num>100</PDBx:auth_seq_num> <PDBx:pdb_mon_id>HOH</PDBx:pdb_mon_id> <PDBx:auth_mon_id>HOH</PDBx:auth_mon_id> <PDBx:pdb_strand_id>C</PDBx:pdb_strand_id> </PDBx:pdbx_nonpoly_scheme> </PDBx:pdbx_nonpoly_schemeCategory> attribute auth_comp_id in category atom_site attribute auth_seq_id in category atom_site Pointer to attribute label_entity_id in category atom_site. Pointer to attribute label_comp_id in category atom_site. NDB residue number. PDB insertion code. PDB residue name. PDB residue number. PDB strand/chain id. Pointer to attribute label_asym_id in category atom_site. 1 A 2B3 Record details about each phasing set: (Note: the phasing set is different from data set. for example: if there are three data sets, the inflection point (IP), the peak (PK) and the high remote (HR), the combination of the phasing set will be IP_iso, PK_iso (the isomorphous repleacement with HR as 'native'), IP_ano, PK_ano and HR_ano (the anomalous difference with itself). Therefore, there are five set used for phasing. Example 1 - three wavelengths <PDBx:pdbx_phasing_MAD_setCategory> <PDBx:pdbx_phasing_MAD_set id="ISO_1"> <PDBx:d_res_low>22.60</PDBx:d_res_low> <PDBx:d_res_high>2.00</PDBx:d_res_high> <PDBx:reflns_acentric>5387</PDBx:reflns_acentric> <PDBx:reflns_centric>471</PDBx:reflns_centric> <PDBx:R_cullis_acentric>0.000</PDBx:R_cullis_acentric> <PDBx:R_cullis_centric>0.000</PDBx:R_cullis_centric> </PDBx:pdbx_phasing_MAD_set> <PDBx:pdbx_phasing_MAD_set id="ISO_2"> <PDBx:d_res_low>22.60</PDBx:d_res_low> <PDBx:d_res_high>2.00</PDBx:d_res_high> <PDBx:reflns_acentric>5365</PDBx:reflns_acentric> <PDBx:reflns_centric>469</PDBx:reflns_centric> <PDBx:R_cullis_acentric>0.803</PDBx:R_cullis_acentric> <PDBx:R_cullis_centric>0.718</PDBx:R_cullis_centric> </PDBx:pdbx_phasing_MAD_set> <PDBx:pdbx_phasing_MAD_set id="ISO_3"> <PDBx:d_res_low>22.60</PDBx:d_res_low> <PDBx:d_res_high>2.00</PDBx:d_res_high> <PDBx:reflns_acentric>5317</PDBx:reflns_acentric> <PDBx:reflns_centric>460</PDBx:reflns_centric> <PDBx:R_cullis_acentric>0.658</PDBx:R_cullis_acentric> <PDBx:R_cullis_centric>0.500</PDBx:R_cullis_centric> </PDBx:pdbx_phasing_MAD_set> <PDBx:pdbx_phasing_MAD_set id="ANO_1"> <PDBx:d_res_low>22.60</PDBx:d_res_low> <PDBx:d_res_high>2.00</PDBx:d_res_high> <PDBx:reflns_acentric>5278</PDBx:reflns_acentric> <PDBx:reflns_centric>0</PDBx:reflns_centric> <PDBx:R_cullis_acentric>0.841</PDBx:R_cullis_acentric> <PDBx:R_cullis_centric>0.000</PDBx:R_cullis_centric> </PDBx:pdbx_phasing_MAD_set> <PDBx:pdbx_phasing_MAD_set id="ANO_2"> <PDBx:d_res_low>22.60</PDBx:d_res_low> <PDBx:d_res_high>2.00</PDBx:d_res_high> <PDBx:reflns_acentric>5083</PDBx:reflns_acentric> <PDBx:reflns_centric>0</PDBx:reflns_centric> <PDBx:R_cullis_acentric>0.649</PDBx:R_cullis_acentric> <PDBx:R_cullis_centric>0.000</PDBx:R_cullis_centric> </PDBx:pdbx_phasing_MAD_set> <PDBx:pdbx_phasing_MAD_set id="ANO_3"> <PDBx:d_res_low>22.60</PDBx:d_res_low> <PDBx:d_res_high>2.00</PDBx:d_res_high> <PDBx:reflns_acentric>5329</PDBx:reflns_acentric> <PDBx:reflns_centric>0</PDBx:reflns_centric> <PDBx:R_cullis_acentric>0.829</PDBx:R_cullis_acentric> <PDBx:R_cullis_centric>0.000</PDBx:R_cullis_centric> </PDBx:pdbx_phasing_MAD_set> </PDBx:pdbx_phasing_MAD_setCategory> attribute R_cullis in category pdbx_phasing_MAD_set records R_cullis for MAD phasing. attribute R_cullis_acentric in category pdbx_phasing_MAD_set records R_cullis using acentric data for MAD phasing. attribute R_cullis_centric in category pdbx_phasing_MAD_set records R_cullis using centric data for MAD phasing. attribute R_kraut in category pdbx_phasing_MAD_set records R_kraut for MAD phasing. attribute r_kraut_acentric in category pdbx_phasing_MAD_set records r_kraut using acentric data for MAD phasing. attribute R_kraut_centric in category pdbx_phasing_MAD_set records r_kraut using centric data for MAD phasing. attribute d_res_high in category pdbx_phasing_MAD_set records the highest resolution for the phasing set. attribute d_res_low in category pdbx_phasing_MAD_set records the lowerest resolution for phasing set. attribute fom in category pdbx_phasing_MAD_set records the figure of merit for MAD phasing. attribute fom_acentric in category pdbx_phasing_MAD_set records the figure of merit using acentric data for MAD phasing. attribute fom_centric in category pdbx_phasing_MAD_set records the figure of merit using centric data for MAD phasing. attribute loc in category pdbx_phasing_MAD_set records lack of closure for MAD phasing. attribute loc_acentric in category pdbx_phasing_MAD_set records lack of closure using acentric data for MAD phasing. attribute loc_centric in category pdbx_phasing_MAD_set records lack of closure using centric data for MAD phasing. attribute number_of_sites in category pdbx_phasing_MAD_set records the number of site refined for the phasing set. attribute power in category pdbx_phasing_MAD_set records phasing power for MAD phasing. attribute power_acentric in category pdbx_phasing_MAD_set records phasing powe using acentric data for MAD phasing. attribute power_centric in category pdbx_phasing_MAD_set records phasing powe using centric data for MAD phasing. attribute reflns in category pdbx_phasing_MAD_set records the number of reflections used for MAD phasing. attribute reflns_acentric in category pdbx_phasing_MAD_set records the number of acentric reflections for MAD phasing. attribute reflns_centric in category pdbx_phasing_MAD_set records the number of centric reflections for MAD phasing. attribute id in category pdbx_phasing_MAD_set records phase set name for MAD phasing. The same as category pdbx_phasing_MAD_set, but broken into shells. Example 1 - three wavelengths (SHARP example) <PDBx:pdbx_phasing_MAD_set_shellCategory> <PDBx:pdbx_phasing_MAD_set_shell id="ISO_1" d_res_low="22.60" d_res_high="7.77"> <PDBx:reflns_acentric>64</PDBx:reflns_acentric> <PDBx:reflns_centric>23</PDBx:reflns_centric> <PDBx:R_cullis_acentric>0.000</PDBx:R_cullis_acentric> <PDBx:R_cullis_centric>0.000</PDBx:R_cullis_centric> <PDBx:power_acentric>0.000</PDBx:power_acentric> <PDBx:power_centric>0.000</PDBx:power_centric> </PDBx:pdbx_phasing_MAD_set_shell> <PDBx:pdbx_phasing_MAD_set_shell id="ISO_1" d_res_low="7.77" d_res_high="5.67"> <PDBx:reflns_acentric>130</PDBx:reflns_acentric> <PDBx:reflns_centric>32</PDBx:reflns_centric> <PDBx:R_cullis_acentric>0.000</PDBx:R_cullis_acentric> <PDBx:R_cullis_centric>0.000</PDBx:R_cullis_centric> <PDBx:power_acentric>0.000</PDBx:power_acentric> <PDBx:power_centric>0.000</PDBx:power_centric> </PDBx:pdbx_phasing_MAD_set_shell> <PDBx:pdbx_phasing_MAD_set_shell id="ISO_1" d_res_low="5.67" d_res_high="4.68"> <PDBx:reflns_acentric>182</PDBx:reflns_acentric> <PDBx:reflns_centric>27</PDBx:reflns_centric> <PDBx:R_cullis_acentric>0.000</PDBx:R_cullis_acentric> <PDBx:R_cullis_centric>0.000</PDBx:R_cullis_centric> <PDBx:power_acentric>0.000</PDBx:power_acentric> <PDBx:power_centric>0.000</PDBx:power_centric> </PDBx:pdbx_phasing_MAD_set_shell> <PDBx:pdbx_phasing_MAD_set_shell id="ISO_1" d_res_low="4.68" d_res_high="4.07"> <PDBx:reflns_acentric>207</PDBx:reflns_acentric> <PDBx:reflns_centric>24</PDBx:reflns_centric> <PDBx:R_cullis_acentric>0.000</PDBx:R_cullis_acentric> <PDBx:R_cullis_centric>0.000</PDBx:R_cullis_centric> <PDBx:power_acentric>0.000</PDBx:power_acentric> <PDBx:power_centric>0.000</PDBx:power_centric> </PDBx:pdbx_phasing_MAD_set_shell> <PDBx:pdbx_phasing_MAD_set_shell id="ANO_1" d_res_low="22.60" d_res_high="7.77"> <PDBx:reflns_acentric>62</PDBx:reflns_acentric> <PDBx:reflns_centric>0</PDBx:reflns_centric> <PDBx:R_cullis_acentric>0.610</PDBx:R_cullis_acentric> <PDBx:R_cullis_centric>0.000</PDBx:R_cullis_centric> <PDBx:power_acentric>1.804</PDBx:power_acentric> <PDBx:power_centric>0.000</PDBx:power_centric> </PDBx:pdbx_phasing_MAD_set_shell> <PDBx:pdbx_phasing_MAD_set_shell id="ANO_1" d_res_low="7.77" d_res_high="5.67"> <PDBx:reflns_acentric>129</PDBx:reflns_acentric> <PDBx:reflns_centric>0</PDBx:reflns_centric> <PDBx:R_cullis_acentric>0.532</PDBx:R_cullis_acentric> <PDBx:R_cullis_centric>0.000</PDBx:R_cullis_centric> <PDBx:power_acentric>2.382</PDBx:power_acentric> <PDBx:power_centric>0.000</PDBx:power_centric> </PDBx:pdbx_phasing_MAD_set_shell> <PDBx:pdbx_phasing_MAD_set_shell id="ANO_1" d_res_low="5.67" d_res_high="4.68"> <PDBx:reflns_acentric>178</PDBx:reflns_acentric> <PDBx:reflns_centric>0</PDBx:reflns_centric> <PDBx:R_cullis_acentric>0.673</PDBx:R_cullis_acentric> <PDBx:R_cullis_centric>0.000</PDBx:R_cullis_centric> <PDBx:power_acentric>1.858</PDBx:power_acentric> <PDBx:power_centric>0.000</PDBx:power_centric> </PDBx:pdbx_phasing_MAD_set_shell> <PDBx:pdbx_phasing_MAD_set_shell id="ANO_1" d_res_low="4.68" d_res_high="4.07"> <PDBx:reflns_acentric>204</PDBx:reflns_acentric> <PDBx:reflns_centric>0</PDBx:reflns_centric> <PDBx:R_cullis_acentric>0.755</PDBx:R_cullis_acentric> <PDBx:R_cullis_centric>0.000</PDBx:R_cullis_centric> <PDBx:power_acentric>1.605</PDBx:power_acentric> <PDBx:power_centric>0.000</PDBx:power_centric> </PDBx:pdbx_phasing_MAD_set_shell> </PDBx:pdbx_phasing_MAD_set_shellCategory> attribute R_cullis in category pdbx_phasing_MAD_set_shell records R_cullis for MAD phasing. attribute R_cullis_acentric in category pdbx_phasing_MAD_set_shell records R_cullis using acentric data for MAD phasing. attribute R_cullis_centric in category pdbx_phasing_MAD_set_shell records R_cullis using centric data for MAD phasing. attribute R_kraut in category pdbx_phasing_MAD_set_shell records R_kraut for MAD phasing. attribute R_kraut_acentric in category pdbx_phasing_MAD_set_shell records R_kraut using acentric data for MAD phasing. attribute R_kraut_centric in category pdbx_phasing_MAD_set_shell records R_kraut using centric data for MAD phasing. attribute fom in category pdbx_phasing_MAD_set_shell records the figure of merit for MAD phasing. attribute fom_acentric in category pdbx_phasing_MAD_set_shell records the figure of merit using acentric data for MAD phasing. attribute fom_centric in category pdbx_phasing_MAD_set_shell records the figure of merit using centric data for MAD phasing. attribute loc in category pdbx_phasing_MAD_set_shell records lack of closure for MAD phasing. attribute loc_acentric in category pdbx_phasing_MAD_set_shell records lack of closure using acentric data for MAD phasing. attribute loc_centric in category pdbx_phasing_MAD_set_shell records lack of closure using centric data for MAD phasing. attribute power in category pdbx_phasing_MAD_set_shell records phasing power for MAD phasing. attribute power_acentric in category pdbx_phasing_MAD_set_shell records phasing powe using acentric data for MAD phasing. attribute power_centric in category pdbx_phasing_MAD_set_shell records phasing powe using centric data for MAD phasing. attribute reflns in category pdbx_phasing_MAD_set_shell records the number of reflections used for MAD phasing. attribute reflns_acentric in category pdbx_phasing_MAD_set_shell records the number of acentric reflections for MAD phasing. attribute reflns_centric in category pdbx_phasing_MAD_set_shell records the number of centric reflections for MAD phasing. attribute id in category pdbx_phasing_MAD_set_shell records phase set name for MAD phasing. attribute d_res_low in category pdbx_phasing_MAD_set_shell records the lowerest resolution for phasing set. attribute d_res_high in category pdbx_phasing_MAD_set_shell records the highest resolution for the phasing set. record the details (coordinates etc.) of anomalous scatters. Example 1 - anomalous scatters is Se <PDBx:pdbx_phasing_MAD_set_siteCategory> <PDBx:pdbx_phasing_MAD_set_site id="1"> <PDBx:atom_type_symbol>SE</PDBx:atom_type_symbol> <PDBx:Cartn_x>25.9407</PDBx:Cartn_x> <PDBx:Cartn_y>-0.103471</PDBx:Cartn_y> <PDBx:Cartn_z>17.4094</PDBx:Cartn_z> </PDBx:pdbx_phasing_MAD_set_site> <PDBx:pdbx_phasing_MAD_set_site id="2"> <PDBx:atom_type_symbol>SE</PDBx:atom_type_symbol> <PDBx:Cartn_x>30.6534</PDBx:Cartn_x> <PDBx:Cartn_y>6.62359</PDBx:Cartn_y> <PDBx:Cartn_z>9.93063</PDBx:Cartn_z> </PDBx:pdbx_phasing_MAD_set_site> <PDBx:pdbx_phasing_MAD_set_site id="3"> <PDBx:atom_type_symbol>SE</PDBx:atom_type_symbol> <PDBx:Cartn_x>-3.26506</PDBx:Cartn_x> <PDBx:Cartn_y>15.5546</PDBx:Cartn_y> <PDBx:Cartn_z>53.9529</PDBx:Cartn_z> </PDBx:pdbx_phasing_MAD_set_site> </PDBx:pdbx_phasing_MAD_set_siteCategory> attribute Cartn_x in category pdbx_phasing_MAD_set_site records the X Cartesian coordinate of site obtained from MAD phasing. attribute Cartn_x_esd in category pdbx_phasing_MAD_set_site records the estimated standard deviation X Cartesian coordinate of site obtained from MAD phasing. attribute Cartn_y in category pdbx_phasing_MAD_set_site records the Y Cartesian coordinate of site obtained from MAD phasing. attribute Cartn_y_esd in category pdbx_phasing_MAD_set_site records the estimated standard deviation Y Cartesian coordinate of site obtained from MAD phasing. attribute Cartn_z in category pdbx_phasing_MAD_set_site records the Z Cartesian coordinate of site obtained from MAD phasing. attribute Cartn_z_esd in category pdbx_phasing_MAD_set_site records the estimated standard deviation Z Cartesian coordinate of site obtained from MAD phasing. attribute atom_type_symbol in category pdbx_phasing_MAD_set_site records the name of site obtained from MAD phasing. attribute b_iso in category pdbx_phasing_MAD_set_site records isotropic temperature factor parameterthe for the site obtained from MAD phasing. attribute b_iso_esd in category pdbx_phasing_MAD_set_site records estimated standard deviation of isotropic temperature factor parameterthe for the site obtained from MAD phasing. attribute fract_x in category pdbx_phasing_MAD_set_site records the X fractional coordinate of site obtained from MAD phasing. attribute fract_x_esd in category pdbx_phasing_MAD_set_site records the estimated standard deviation X fractional coordinate of site obtained from MAD phasing. attribute fract_y in category pdbx_phasing_MAD_set_site records the Y fractional coordinate of site obtained from MAD phasing. attribute fract_y_esd in category pdbx_phasing_MAD_set_site records the estimated standard deviation Y fractional coordinate of site obtained from MAD phasing. attribute fract_z in category pdbx_phasing_MAD_set_site records the Z fractional coordinate of site obtained from MAD phasing. attribute fract_z_esd in category pdbx_phasing_MAD_set_site records the estimated standard deviation Z fractional coordinate of site obtained from MAD phasing. attribute occupancy in category pdbx_phasing_MAD_set_site records the fraction of the atom type presented at this site. attribute occupancy_esd in category pdbx_phasing_MAD_set_site records estimated standard deviation of the fraction of the atom type presented at this site. The relative real isotropic occupancy of the atom type present at this heavy-atom site in a given atom site. record the phasing set. attribute id in category pdbx_phasing_MAD_set_site records the number of site obtained from MAD phasing. Data items in the PDBX_PHASING_MAD_SHELL category record details about the phasing of the structure, when methods involving multiple anomalous dispersion techniques are involved (note: the values are overall, but broken down into shells of resolution) Example 1 - <PDBx:pdbx_phasing_MAD_shellCategory> <PDBx:pdbx_phasing_MAD_shell d_res_low="22.60" d_res_high="7.77"> <PDBx:reflns_acentric>64</PDBx:reflns_acentric> <PDBx:fom_acentric>0.886</PDBx:fom_acentric> <PDBx:reflns_centric>23</PDBx:reflns_centric> <PDBx:fom_centric>0.641</PDBx:fom_centric> </PDBx:pdbx_phasing_MAD_shell> <PDBx:pdbx_phasing_MAD_shell d_res_low="7.77" d_res_high="5.67"> <PDBx:reflns_acentric>132</PDBx:reflns_acentric> <PDBx:fom_acentric>0.863</PDBx:fom_acentric> <PDBx:reflns_centric>32</PDBx:reflns_centric> <PDBx:fom_centric>0.642</PDBx:fom_centric> </PDBx:pdbx_phasing_MAD_shell> <PDBx:pdbx_phasing_MAD_shell d_res_low="5.67" d_res_high="4.68"> <PDBx:reflns_acentric>182</PDBx:reflns_acentric> <PDBx:fom_acentric>0.842</PDBx:fom_acentric> <PDBx:reflns_centric>27</PDBx:reflns_centric> <PDBx:fom_centric>0.737</PDBx:fom_centric> </PDBx:pdbx_phasing_MAD_shell> <PDBx:pdbx_phasing_MAD_shell d_res_low="4.68" d_res_high="4.07"> <PDBx:reflns_acentric>209</PDBx:reflns_acentric> <PDBx:fom_acentric>0.789</PDBx:fom_acentric> <PDBx:reflns_centric>24</PDBx:reflns_centric> <PDBx:fom_centric>0.682</PDBx:fom_centric> </PDBx:pdbx_phasing_MAD_shell> <PDBx:pdbx_phasing_MAD_shell d_res_low="4.07" d_res_high="3.65"> <PDBx:reflns_acentric>246</PDBx:reflns_acentric> <PDBx:fom_acentric>0.772</PDBx:fom_acentric> <PDBx:reflns_centric>27</PDBx:reflns_centric> <PDBx:fom_centric>0.633</PDBx:fom_centric> </PDBx:pdbx_phasing_MAD_shell> <PDBx:pdbx_phasing_MAD_shell d_res_low="3.65" d_res_high="3.34"> <PDBx:reflns_acentric>260</PDBx:reflns_acentric> <PDBx:fom_acentric>0.752</PDBx:fom_acentric> <PDBx:reflns_centric>31</PDBx:reflns_centric> <PDBx:fom_centric>0.700</PDBx:fom_centric> </PDBx:pdbx_phasing_MAD_shell> </PDBx:pdbx_phasing_MAD_shellCategory> attribute R_cullis in category pdbx_phasing_MAD_shell records R_cullis for MAD phasing. attribute R_cullis_acentric in category pdbx_phasing_MAD_shell records R_cullis using acentric data for MAD phasing. attribute R_cullis_centric in category pdbx_phasing_MAD_shell records R_cullis using centric data for MAD phasing. attribute R_kraut in category pdbx_phasing_MAD_shell records R_kraut for MAD phasing. attribute r_kraut_acentric in category pdbx_phasing_MAD_shell records R_kraut using acentric data for MAD phasing. attribute R_kraut_centric in category pdbx_phasing_MAD_shell records R_kraut using centric data for MAD phasing. attribute fom in category pdbx_phasing_MAD_shell records the figure of merit for MAD phasing. attribute fom_acentric in category pdbx_phasing_MAD_shell records the figure of merit using acentric data for MAD phasing. attribute fom_centric in category pdbx_phasing_MAD_shell records the figure of merit using centric data for MAD phasing. attribute loc in category pdbx_phasing_MAD_shell records lack of closure for MAD phasing. attribute loc_acentric in category pdbx_phasing_MAD_shell records lack of closure using acentric data for MAD phasing. attribute loc_centric in category pdbx_phasing_MAD_shell records lack of closure using centric data for MAD phasing. attribute loc in category pdbx_phasing_MAD_shell records phasing power for MAD phasing. attribute power_acentric in category pdbx_phasing_MAD_shell records phasing powe using acentric data for MAD phasing. attribute power_centric in category pdbx_phasing_MAD_shell records phasing powe using centric data for MAD phasing. attribute reflns in category pdbx_phasing_MAD_shell records the number of reflections used for MAD phasing. attribute reflns_acentric in category pdbx_phasing_MAD_shell records the number of acentric reflections for MAD phasing. attribute reflns_centric in category pdbx_phasing_MAD_shell records the number of centric reflections for MAD phasing. attribute d_res_low in category pdbx_phasing_MAD_shell records the lower resolution for the shell. attribute d_res_high in category pdbx_phasing_MAD_shell records the higher resolution for the shell. Data items in the PDBX_PHASING_MR category record details about molecular replacement. Example 1 - molecular replacement example from program CNS. <PDBx:pdbx_phasing_MRCategory> <PDBx:pdbx_phasing_MR entry_id="ABC001"> <PDBx:method_rotation>real-space rotation search</PDBx:method_rotation> <PDBx:d_res_high_rotation>3.8</PDBx:d_res_high_rotation> <PDBx:d_res_low_rotation>13.0</PDBx:d_res_low_rotation> <PDBx:sigma_F_rotation>1.0</PDBx:sigma_F_rotation> <PDBx:reflns_percent_rotation>97.8</PDBx:reflns_percent_rotation> <PDBx:method_translation>gerneral using PC-refinement= e2e2</PDBx:method_translation> <PDBx:d_res_high_translation>4.0</PDBx:d_res_high_translation> <PDBx:d_res_low_translation>15.0</PDBx:d_res_low_translation> <PDBx:sigma_F_translation>0</PDBx:sigma_F_translation> <PDBx:reflns_percent_translation>97.7</PDBx:reflns_percent_translation> <PDBx:correlation_coeff_Fo_to_Fc>0.586</PDBx:correlation_coeff_Fo_to_Fc> <PDBx:packing>0.3086</PDBx:packing> </PDBx:pdbx_phasing_MR> </PDBx:pdbx_phasing_MRCategory> The value of attribute R_factor in category pdbx_phasing_MR identifies the R factor (defined as uasual) after rotation and translation. The value of attribute R_rigid_body in category pdbx_phasing_MR identifies the R factor for rigid body refinement after rotation and translation.(In general, rigid body refinement has to be carried out after molecular replacement. The value of attribute correlation_coeff_Fo_to_Fc in category pdbx_phasing_MR identifies the correlation between the observed and the calculated structure factor after rotation and translation. The value of attribute correlation_coeff_Io_to_Ic in category pdbx_phasing_MR identifies the correlation between the observed and the calculated intensity (~|F|^2) after rotation and translation. The value of attribute d_res_high_rotation in category pdbx_phasing_MR identifies the highest resolution used for rotation search. The value of attribute d_res_high_translation in category pdbx_phasing_MR identifies the highest resolution used for translation search. The value of attribute d_res_low_rotation in category pdbx_phasing_MR identifies the lowest resolution used for rotation search. The value of attribute d_res_low_translation in category pdbx_phasing_MR identifies the lowest resolution used for translation search. The value of attribute method_rotation in category pdbx_phasing_MR identifies the method used for rotation search. For example, the rotation method may be realspace, fastdirect, or direct. . The value of attribute method_translation in category pdbx_phasing_MR identifies the method used for translation search. For example in CNS, the translation method may be "general" or "phased" with PC refinement target using "fastf2f2" "e2e2" "e1e1" "f2f2" "f1f1" "residual" "vector". . The value of attribute model_details in category pdbx_phasing_MR records the details of model used. For example, the original model can be truncated by deleting side chains, doubtful parts, using the monomer if the original model was an oligomer. The search model may be one domain of a large molecule. What is the pdb IDs. The value of attribute packing in category pdbx_phasing_MR identifies the packing of search model in the unit cell. Too much crystallographic contacts may indicate a bad search. The value of attribute reflns_percent_rotation in category pdbx_phasing_MR identifies the completness of data used for rotation search. The value of attribute reflns_percent_translation in category pdbx_phasing_MR identifies the completness of data used for translation search. The value of attribute sigma_F_rotation in category pdbx_phasing_MR identifies the sigma cut off of structure factor used for rotation search. The value of attribute sigma_F_translation in category pdbx_phasing_MR identifies the sigma cut off of structure factor used for translation search. The value of attribute sigma_I_rotation in category pdbx_phasing_MR identifies the sigma cut off of intensity used for rotation search. The value of attribute sigma_I_translation in category pdbx_phasing_MR identifies the sigma cut off of intensity used for translation search. The value of attribute entry_id in category pdbx_phasing_MR identifies the data block. Data items in the PDBX_PHASING_DM category record details about density modification Example 1 - density modification from resolve <PDBx:pdbx_phasing_dmCategory> <PDBx:pdbx_phasing_dm entry_id="ABC001"> <PDBx:fom_acentric>0.85</PDBx:fom_acentric> <PDBx:fom_centric>0.79</PDBx:fom_centric> <PDBx:fom>0.85</PDBx:fom> <PDBx:reflns_acentric>11351</PDBx:reflns_acentric> <PDBx:reflns_centric>1135</PDBx:reflns_centric> <PDBx:reflns>12486</PDBx:reflns> </PDBx:pdbx_phasing_dm> </PDBx:pdbx_phasing_dmCategory> The value of attribute delta_phi_final in category pdbx_phasing_dm identifies phase difference after density modification The value of attribute delta_phi_initial in category pdbx_phasing_dm identifies phase difference before density modification The value of attribute fom in category pdbx_phasing_dm identifies the figure of merit for all the data The value of attribute fom_acentric in category pdbx_phasing_dm identifies the figure of merit for acentric data The value of attribute fom_centric in category pdbx_phasing_dm identifies the figure of merit for acentric data The value of attribute mask_type in category pdbx_phasing_dm identifies the type of mask used for density modification The value of attribute method in category pdbx_phasing_dm identifies the method used for density modification The value of attribute reflns in category pdbx_phasing_dm identifies the number of centric and acentric reflections. The value of attribute reflns_acentric in category pdbx_phasing_dm identifies the number of acentric reflections. The value of attribute reflns_centric in category pdbx_phasing_dm identifies the number of centric reflections. The value of attribute entry_id in category pdbx_phasing_dm identifies the data block. Data items in the PDBX_PHASING_DM_SHELL category record details about density modification in resolution shell. Example 1 - density modification with shells <PDBx:pdbx_phasing_dm_shellCategory> <PDBx:pdbx_phasing_dm_shell d_res_low="100.00" d_res_high="7.73"> <PDBx:reflns>502</PDBx:reflns> <PDBx:fom>0.879</PDBx:fom> <PDBx:delta_phi_final>24.7</PDBx:delta_phi_final> </PDBx:pdbx_phasing_dm_shell> <PDBx:pdbx_phasing_dm_shell d_res_low="7.73" d_res_high="6.24"> <PDBx:reflns>506</PDBx:reflns> <PDBx:fom>0.857</PDBx:fom> <PDBx:delta_phi_final>29.2</PDBx:delta_phi_final> </PDBx:pdbx_phasing_dm_shell> <PDBx:pdbx_phasing_dm_shell d_res_low="6.24" d_res_high="5.50"> <PDBx:reflns>504</PDBx:reflns> <PDBx:fom>0.838</PDBx:fom> <PDBx:delta_phi_final>29.2</PDBx:delta_phi_final> </PDBx:pdbx_phasing_dm_shell> <PDBx:pdbx_phasing_dm_shell d_res_low="5.50" d_res_high="5.02"> <PDBx:reflns>502</PDBx:reflns> <PDBx:fom>0.851</PDBx:fom> <PDBx:delta_phi_final>25.3</PDBx:delta_phi_final> </PDBx:pdbx_phasing_dm_shell> <PDBx:pdbx_phasing_dm_shell d_res_low="5.02" d_res_high="4.67"> <PDBx:reflns>503</PDBx:reflns> <PDBx:fom>0.831</PDBx:fom> <PDBx:delta_phi_final>22.7</PDBx:delta_phi_final> </PDBx:pdbx_phasing_dm_shell> </PDBx:pdbx_phasing_dm_shellCategory> The value of attribute delta_phi_final in category pdbx_phasing_dm_shell identifies phase difference after density modification with resolution shells. The value of attribute delta_phi_initial in category pdbx_phasing_dm_shell identifies phase difference before density modification with resolution shells. The value of attribute fom in category pdbx_phasing_dm_shell identifies the figure of merit for all the data with resolution shells. The value of attribute fom_acentric in category pdbx_phasing_dm_shell identifies the figure of merit for acentric data with resolution shells The value of attribute fom_centric in category pdbx_phasing_dm_shell identifies the figure of merit for centric data with resolution shells. The value of attribute reflns in category pdbx_phasing_dm_shell identifies the number of centric and acentric reflections with resolution shells. The value of attribute reflns_acentric in category pdbx_phasing_dm_shell identifies the number of acentric reflections with resolution shells. The value of attribute reflns_centric in category pdbx_phasing_dm_shell identifies the number of centric reflections with resolution shells. The value of attribute d_res_low in category pdbx_phasing_dm_shell identifies low resolution The value of attribute d_res_high in category pdbx_phasing_dm_shell identifies high resolution The PDBX_POLY_SEQ_SCHEME category provides residue level nomenclature mapping for polymer entities. Example 1 - based on NDB entry DDFB25 <PDBx:pdbx_poly_seq_schemeCategory> <PDBx:pdbx_poly_seq_scheme asym_id="A" entity_id="1" seq_id="1" mon_id="C"> <PDBx:pdb_mon_id>C</PDBx:pdb_mon_id> <PDBx:auth_mon_id>C</PDBx:auth_mon_id> <PDBx:pdb_strand_id>A</PDBx:pdb_strand_id> </PDBx:pdbx_poly_seq_scheme> <PDBx:pdbx_poly_seq_scheme asym_id="A" entity_id="1" seq_id="2" mon_id="G"> <PDBx:pdb_mon_id>G</PDBx:pdb_mon_id> <PDBx:auth_mon_id>G</PDBx:auth_mon_id> <PDBx:pdb_strand_id>A</PDBx:pdb_strand_id> </PDBx:pdbx_poly_seq_scheme> <PDBx:pdbx_poly_seq_scheme asym_id="A" entity_id="1" seq_id="3" mon_id="T"> <PDBx:pdb_mon_id>T</PDBx:pdb_mon_id> <PDBx:auth_mon_id>T</PDBx:auth_mon_id> <PDBx:pdb_strand_id>A</PDBx:pdb_strand_id> </PDBx:pdbx_poly_seq_scheme> <PDBx:pdbx_poly_seq_scheme asym_id="A" entity_id="1" seq_id="4" mon_id="+A"> <PDBx:pdb_mon_id>+A</PDBx:pdb_mon_id> <PDBx:auth_mon_id>+A</PDBx:auth_mon_id> <PDBx:pdb_strand_id>A</PDBx:pdb_strand_id> </PDBx:pdbx_poly_seq_scheme> <PDBx:pdbx_poly_seq_scheme asym_id="A" entity_id="1" seq_id="5" mon_id="C"> <PDBx:pdb_mon_id>C</PDBx:pdb_mon_id> <PDBx:auth_mon_id>C</PDBx:auth_mon_id> <PDBx:pdb_strand_id>A</PDBx:pdb_strand_id> </PDBx:pdbx_poly_seq_scheme> <PDBx:pdbx_poly_seq_scheme asym_id="A" entity_id="1" seq_id="6" mon_id="G"> <PDBx:pdb_mon_id>G</PDBx:pdb_mon_id> <PDBx:auth_mon_id>G</PDBx:auth_mon_id> <PDBx:pdb_strand_id>A</PDBx:pdb_strand_id> </PDBx:pdbx_poly_seq_scheme> </PDBx:pdbx_poly_seq_schemeCategory> attribute auth_comp_id in category atom_site attribute auth_seq_id in category atom_site NDB residue number. PDB insertion code. PDB residue name. PDB residue number. PDB strand/chain id. Pointer to attribute label_asym_id in category atom_site. 1 A 2B3 Pointer to attribute id in category entity. Pointer to attribute num in category entity_poly_seq Pointer to attribute mon_id in category entity_poly_seq. This category provides a placeholder for pre-release sequence information. After release this category should be discarded. <PDBx:pdbx_prerelease_seqCategory> <PDBx:pdbx_prerelease_seq entity_id="1"> <PDBx:seq_one_letter_code>GKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGAAFNVEFD</PDBx:seq_one_letter_code> </PDBx:pdbx_prerelease_seq> <PDBx:pdbx_prerelease_seq entity_id="2"> <PDBx:seq_one_letter_code>HKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNN</PDBx:seq_one_letter_code> </PDBx:pdbx_prerelease_seq> </PDBx:pdbx_prerelease_seqCategory> Chemical sequence expressed as string of one-letter amino acid codes. A for alanine or adenine B for ambiguous asparagine/aspartic-acid R for arginine N for asparagine D for aspartic-acid C for cysteine or cystine or cytosine Q for glutamine E for glutamic-acid Z for ambiguous glutamine/glutamic acid G for glycine or guanine H for histidine I for isoleucine L for leucine K for lysine M for methionine F for phenylalanine P for proline S for serine T for threonine or thymine W for tryptophan Y for tyrosine V for valine U for uracil MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGAAFNVEFD This data item is a pointer to attribute id in category entity in the ENTITY category. Data items in the PDBX_REFINE category record details about additional structure refinement parameters which are needed to complete legacy REMARK 3 refinement templates in PDB format files. Example 1 - PDB placeholders for refinement program SHELX <PDBx:pdbx_refineCategory> <PDBx:pdbx_refine entry_id="ABC001"> <PDBx:R_factor_all_4sig_cutoff>0.174</PDBx:R_factor_all_4sig_cutoff> <PDBx:R_factor_obs_4sig_cutoff>0.169</PDBx:R_factor_obs_4sig_cutoff> <PDBx:number_reflns_obs_4sig_cutoff>1263</PDBx:number_reflns_obs_4sig_cutoff> <PDBx:free_R_factor_4sig_cutoff>0.216</PDBx:free_R_factor_4sig_cutoff> <PDBx:free_R_val_test_set_ct_4sig_cutoff>164</PDBx:free_R_val_test_set_ct_4sig_cutoff> <PDBx:free_R_val_test_set_size_perc_4sig_cutoff>1.29</PDBx:free_R_val_test_set_size_perc_4sig_cutoff> </PDBx:pdbx_refine> </PDBx:pdbx_refineCategory> R-value (all reflections, 4 sigma cutoff) Placeholder for PDB mapping of SHELXL refinement data. 0.174 R-value (all reflections, no cutoff) Placeholder for PDB mapping of SHELXL refinement data. R-value (working set, 4 sigma cutoff) Placeholder for PDB mapping of SHELXL refinement data. 0.169 R-value (working set reflections, no cutoff) Placeholder for PDB mapping of SHELXL refinement data. R free value (4 sigma cutoff). Placeholder for PDB mapping of SHELXL refinement data. 0.216 Free R-value (no cutoff) Placeholder for PDB mapping of SHELXL refinement data. Free R-value (4 sigma cutoff) Placeholder for PDB mapping of SHELXL refinement data. Free R-value test set count (4 sigma cutoff) Placeholder for PDB mapping of SHELXL refinement data. 164 Free R-value test set count (no cutoff) Placeholder for PDB mapping of SHELXL refinement data. Free R-value test set size (in percent, 4 sigma cutoff) Placeholder for PDB mapping of SHELXL refinement data. 1.29 Free R-value test set size (in percent, no cutoff) Placeholder for PDB mapping of SHELXL refinement data. Total number of reflections (4 sigma cutoff). Placeholder for PDB mapping of SHELXL refinement data. 1263 Total number of reflections (no cutoff). Placeholder for PDB mapping of SHELXL refinement data. This data item is a pointer to attribute id in category entry in the ENTRY category. Auxilary parameter and topology files used in refinement. <PDBx:pdbx_refine_aux_fileCategory> <PDBx:pdbx_refine_aux_file serial_no="1"> <PDBx:file_name>parm_hol.dat</PDBx:file_name> <PDBx:file_type>PARAMETER</PDBx:file_type> </PDBx:pdbx_refine_aux_file> </PDBx:pdbx_refine_aux_fileCategory> Auxilary file name. PARAM_NDBX_HIGH.DNA Auxilary file type. PARAMETER Serial number. Data items in the REFINE_TLS category record details about TLS parameters used in structure refinement. Note that the intention is primarily to describe directly refined TLS parameters, although other methods of obtaining TLS parameters may be covered, see item attribute method in category pdbx_refine_tls The [1][1] element of the libration tensor L. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. The estimated standard deviation of attribute L[1][1] in category pdbx_refine_tls. The [1][2] element of the libration tensor L. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. The estimated standard deviation of attribute L[1][2] in category pdbx_refine_tls. The [1][3] element of the libration tensor L. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. The estimated standard deviation of attribute L[1][3] in category pdbx_refine_tls. The [2][2] element of the libration tensor L. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. The estimated standard deviation of attribute L[2][2] in category pdbx_refine_tls. The [2][3] element of the libration tensor L. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. The estimated standard deviation of attribute L[2][3] in category pdbx_refine_tls. The [3][3] element of the libration tensor L. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. The estimated standard deviation of attribute L[3][3] in category pdbx_refine_tls. The [1][1] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. The trace of S is indeterminate by crystallography, and should be set to zero. The estimated standard deviation of attribute S[1][1] in category pdbx_refine_tls. The [1][2] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric The estimated standard deviation of attribute S[1][2] in category pdbx_refine_tls. The [1][3] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric The estimated standard deviation of attribute S[1][3] in category pdbx_refine_tls. The [2][1] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric The estimated standard deviation of attribute S[2][1] in category pdbx_refine_tls. The [2][2] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. The trace of S is indeterminate by crystallography, and should be set to zero. The estimated standard deviation of attribute S[2][2] in category pdbx_refine_tls. The [2][3] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric The estimated standard deviation of attribute S[2][3] in category pdbx_refine_tls. The [3][1] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric The estimated standard deviation of attribute S[3][1] in category pdbx_refine_tls. The [3][2] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric The estimated standard deviation of attribute S[3][2] in category pdbx_refine_tls. The [3][3] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. The trace of S is indeterminate by crystallography, and should be set to zero. The estimated standard deviation of attribute S[3][3] in category pdbx_refine_tls. The [1][1] element of the translation tensor T. This should be given in the same coordinate frame and units as the corresponding anisotropic displacement parameters. The estimated standard deviation of attribute T[1][1] in category pdbx_refine_tls. The [1][2] element of the translation tensor T. This should be given in the same coordinate frame and units as the corresponding anisotropic displacement parameters. The estimated standard deviation of attribute T[1][2] in category pdbx_refine_tls. The [1][3] element of the translation tensor T. This should be given in the same coordinate frame and units as the corresponding anisotropic displacement parameters. The estimated standard deviation of attribute T[1][3] in category pdbx_refine_tls. The [2][2] element of the translation tensor T. This should be given in the same coordinate frame and units as the corresponding anisotropic displacement parameters. The estimated standard deviation of attribute T[2][2] in category pdbx_refine_tls. The [2][3] element of the translation tensor T. This should be given in the same coordinate frame and units as the corresponding anisotropic displacement parameters. The estimated standard deviation of attribute T[2][3] in category pdbx_refine_tls. The [3][3] element of the translation tensor T. This should be given in the same coordinate frame and units as the corresponding anisotropic displacement parameters. The estimated standard deviation of attribute T[3][3] in category pdbx_refine_tls. A description of the TLS group, such as a domain name or a chemical group name. Chain A catalytic domain Chain A Tyr 56 side chain The method by which the TLS parameters were obtained. The x coordinate in angstroms of the origin to which the TLS parameters are referred, specified according to a set of orthogonal Cartesian axes related to the cell axes as given in attribute Cartn_transform_axes. in category atom_sites If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric The y coordinate in angstroms of the origin to which the TLS parameters are referred, specified according to a set of orthogonal Cartesian axes related to the cell axes as given in attribute Cartn_transform_axes. in category atom_sites If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric The z coordinate in angstroms of the origin to which the TLS parameters are referred, specified according to a set of orthogonal Cartesian axes related to the cell axes as given in attribute Cartn_transform_axes. in category atom_sites If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric The value of attribute id in category pdbx_refine_tls must uniquely identify a record in the PDBX_REFINE_TLS list. Note that this item need not be a number; it can be any unique identifier. 1 A Data items in the PDBX_REFINE_TLS_GROUP category record details about a fragment of a TLS group. Properties of the TLS group are recorded in PDBX_REFINE_TLS A component of the identifier for the residue at which the TLS fragment range begins. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. 1 5A A component of the identifier for the residue at which the TLS fragment range begins. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. O 2B3 A component of the identifier for the residue at which the TLS fragment range begins. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. 1 303 A component of the identifier for the residue at which the TLS fragment range ends. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. 1 5A A component of the identifier for the residue at which the TLS fragment range ends. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. O 2B3 A component of the identifier for the residue at which the TLS fragment range ends. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. 1 303 This data item is a pointer to attribute id in category pdbx_refine_tls in the REFINE_TLS category. A description of the subset of atoms in the specified range included in the TLS fragment. The value of attribute id in category pdbx_refine_tls_group must uniquely identify a record in the REFINE_TLS_GROUP list. Note that this item need not be a number; it can be any unique identifier. 1 A The details about each robotic system used to collect data for this project. The name of the manufacturer of the robotic system. The model of the robotic system. The type of robotic system used for in the production pathway. Assign a numerical ID to each instrument. Data items in the PDBX_STRUCT_SHEET_HBOND category record details about the hydrogen bonding between residue ranges in a beta sheet. This category is provided for cases where only a single hydrogen bond is used to register the two residue ranges. Category STRUCT_SHEET_HBOND should be used when the initial and terminal hydrogen bonds for strand pair are known. A component of the residue identifier for the first partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. A component of the residue identifier for the first partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. A component of the residue identifier for the first partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. A component of the residue identifier for the first partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. A component of the residue identifier for the first partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. A component of the residue identifier for the first partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. A component of the residue identifier for the first partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. A component of the residue identifier for the first partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. A component of the residue identifier for the first partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. A component of the residue identifier for the second partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. A component of the residue identifier for the second partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. A component of the residue identifier for the second partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. A component of the residue identifier for the second partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. A component of the residue identifier for the second partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. A component of the residue identifier for the second partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. A component of the residue identifier for the second partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. A component of the residue identifier for the second partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. A component of the residue identifier for the second partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. This data item is a pointer to attribute id in category struct_sheet in the STRUCT_SHEET category. This data item is a pointer to attribute id in category struct_sheet_range in the STRUCT_SHEET_RANGE category. This data item is a pointer to attribute id in category struct_sheet_range in the STRUCT_SHEET_RANGE category. Parameter and topology files used in X-PLOR/CNS refinement. <PDBx:pdbx_xplor_fileCategory> <PDBx:pdbx_xplor_file serial_no="1"> <PDBx:param_file>parm_hol.dat</PDBx:param_file> <PDBx:topol_file>topol_hol.dat</PDBx:topol_file> </PDBx:pdbx_xplor_file> </PDBx:pdbx_xplor_fileCategory> Parameter file name in X-PLOR/CNS refinement. PARAM_NDBX_HIGH.DNA Topology file name in X-PLOR/CNS refinement. TOP_NDBX.DNA Serial number. Data items in the PHASING category record details about the phasing of the structure, listing the various methods used in the phasing process. The details about the application of each method are listed in the appropriate subcategories. Example 1 - example is completely hypothetical <PDBx:phasingCategory> <PDBx:phasing method="mir"></PDBx:phasing> <PDBx:phasing method="averaging"></PDBx:phasing> </PDBx:phasingCategory> A listing of the method or methods applied to phase this structure. phasing by ab initio methods abinitio phase improvement by averaging over multiple images of the structure averaging phasing by direct methods dm phasing by iterative single wavelength anomalous scattering isas phasing by iterative single wavelength anomalous scattering isir phasing beginning with phases calculated from an isomorphous structure isomorphous phasing by multiple-wavelength anomalous dispersion mad phasing by multiple isomorphous replacement mir phasing by multiple isomorphous replacement with anomalous scattering miras phasing by molecular replacement mr phasing by single isomorphous replacement sir phasing by single isomorphous replacement with anomalous scattering. siras Data items in the PHASING_MAD category record details about the phasing of the structure, when methods involving multiple anomalous dispersion techniques are involved. Example 1 - based on a paper by Shapiro et al. [(1995). Nature (London), 374, 327-337] <PDBx:phasing_MADCategory> <PDBx:phasing_MAD entry_id="NCAD"></PDBx:phasing_MAD> </PDBx:phasing_MADCategory> A description of special aspects of the MAD phasing. A description of the MAD phasing method applied to phase this structure. Note that this is not the computer program used, which is described in the SOFTWARE category, but rather the method itself. This data item should be used to describe significant methodological options used within the MAD phasing program. phasing_MAD.pdbx_R_cullis records R_cullis for MAD phasing. attribute pdbx_R_cullis_acentric in category phasing_MAD records R_cullis using acentric data for MAD phasing. attribute pdbx_R_cullis_centric in category phasing_MAD records R_cullis using centric data for MAD phasing. attribute pdbx_R_kraut in category phasing_MAD records R_kraut for MAD phasing. attribute pdbx_R_kraut_acentric in category phasing_MAD records R_kraut using acentric data for MAD phasing. attribute pdbx_R_kraut_centric in category phasing_MAD records R_kraut using centric data for MAD phasing. attribute pdbx_d_res_high in category phasing_MAD records the highest resolution for MAD phasing. attribute pdbx_d_res_low in category phasing_MAD records the lowest resolution for MAD phasing. attribute pdbx_fom in category phasing_MAD records the figure of merit for MAD phasing. attribute pdbx_fom_acentric in category phasing_MAD records the figure of merit using acentric data for MAD phasing. attribute pdbx_fom_centric in category phasing_MAD records the figure of merit using centric data for MAD phasing. phasing_MAD.pdbx_loc records lack of closure for MAD phasing. phasing_MAD.pdbx_loc_acentric records lack of closure using acentric data for MAD phasing. phasing_MAD.pdbx_loc_centric records lack of closure using centric data for MAD phasing. phasing_MAD.pdbx_loc records phasing power for MAD phasing. phasing_MAD.pdbx_power_acentric records phasing powe using acentric data for MAD phasing. phasing_MAD.pdbx_power_centric records phasing powe using centric data for MAD phasing. attribute pdbx_reflns in category phasing_MAD records the number of reflections used for MAD phasing. attribute pdbx_reflns_acentric in category phasing_MAD records the number of acentric reflections for MAD phasing. attribute pdbx_reflns_centric in category phasing_MAD records the number of centric reflections for MAD phasing. This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the PHASING_MAD_CLUST category record details about a cluster of experiments that contributed to the generation of a set of phases. Example 1 - based on a paper by Shapiro et al. [(1995). Nature (London), 374, 327-337] <PDBx:phasing_MAD_clustCategory> <PDBx:phasing_MAD_clust id="four wavelength" expt_id="1"> <PDBx:number_set>4</PDBx:number_set> </PDBx:phasing_MAD_clust> <PDBx:phasing_MAD_clust id="five wavelength" expt_id="1"> <PDBx:number_set>5</PDBx:number_set> </PDBx:phasing_MAD_clust> <PDBx:phasing_MAD_clust id="five wavelength" expt_id="2"> <PDBx:number_set>5</PDBx:number_set> </PDBx:phasing_MAD_clust> </PDBx:phasing_MAD_clustCategory> The number of data sets in this cluster of data sets. This data item is a pointer to attribute id in category phasing_MAD_expt in the PHASING_MAD_EXPT category. The value of attribute id in category phasing_MAD_clust must, together with attribute expt_id in category phasing_MAD_clust uniquely identify a record in the PHASING_MAD_CLUST list. Note that this item need not be a number; it can be any unique identifier. Data items in the PHASING_MAD_EXPT category record details about a MAD phasing experiment, such as the number of experiments that were clustered together to produce a set of phases, the statistics for those phases, and so on. Example 1 - based on a paper by Shapiro et al. [(1995). Nature (London), 374, 327-337] <PDBx:phasing_MAD_exptCategory> <PDBx:phasing_MAD_expt id="1"> <PDBx:number_clust>2</PDBx:number_clust> <PDBx:R_normal_all>0.063</PDBx:R_normal_all> <PDBx:R_normal_anom_scat>0.451</PDBx:R_normal_anom_scat> <PDBx:delta_delta_phi>58.5</PDBx:delta_delta_phi> <PDBx:delta_phi_sigma>20.3</PDBx:delta_phi_sigma> <PDBx:mean_fom>0.88</PDBx:mean_fom> </PDBx:phasing_MAD_expt> <PDBx:phasing_MAD_expt id="2"> <PDBx:number_clust>1</PDBx:number_clust> <PDBx:R_normal_all>0.051</PDBx:R_normal_all> <PDBx:R_normal_anom_scat>0.419</PDBx:R_normal_anom_scat> <PDBx:delta_delta_phi>36.8</PDBx:delta_delta_phi> <PDBx:delta_phi_sigma>18.2</PDBx:delta_phi_sigma> <PDBx:mean_fom>0.93</PDBx:mean_fom> </PDBx:phasing_MAD_expt> </PDBx:phasing_MAD_exptCategory> Definition... Definition... The difference between two independent determinations of attribute delta_phi in category phasing_MAD_expt. The phase difference between F~t~(h), the structure factor due to normal scattering from all atoms, and F~a~(h), the structure factor due to normal scattering from only the anomalous scatterers. The estimated standard deviation of attribute delta_phi in category phasing_MAD_expt. The mean figure of merit. The number of clusters of data sets in this phasing experiment. The value of attribute id in category phasing_MAD_expt must uniquely identify each record in the PHASING_MAD_EXPT list. Data items in the PHASING_MAD_RATIO category record the ratios of phasing statistics between pairs of data sets in a MAD phasing experiment, in given shells of resolution. Example 1 - based on a paper by Shapiro et al. [(1995). Nature (London), 374, 327-337] <PDBx:phasing_MAD_ratioCategory> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="four wavelength" wavelength_1="1.4013" wavelength_2="1.4013"> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:ratio_one_wl>0.084</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.076</PDBx:ratio_one_wl_centric> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="four wavelength" wavelength_1="1.4013" wavelength_2="1.3857"> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.067</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="four wavelength" wavelength_1="1.4013" wavelength_2="1.3852"> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.051</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="four wavelength" wavelength_1="1.4013" wavelength_2="1.3847"> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.044</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="four wavelength" wavelength_1="1.3857" wavelength_2="1.3857"> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:ratio_one_wl>0.110</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.049</PDBx:ratio_one_wl_centric> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="four wavelength" wavelength_1="1.3857" wavelength_2="1.3852"> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.049</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="four wavelength" wavelength_1="1.3857" wavelength_2="1.3847"> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.067</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="four wavelength" wavelength_1="1.3852" wavelength_2="1.3852"> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:ratio_one_wl>0.149</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.072</PDBx:ratio_one_wl_centric> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="four wavelength" wavelength_1="1.3852" wavelength_2="1.3847"> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.039</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="four wavelength" wavelength_1="1.3847" wavelength_2="1.3847"> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:ratio_one_wl>0.102</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.071</PDBx:ratio_one_wl_centric> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="four wavelength" wavelength_1="1.4013" wavelength_2="1.4013"> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:ratio_one_wl>0.114</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.111</PDBx:ratio_one_wl_centric> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="four wavelength" wavelength_1="1.4013" wavelength_2="1.3857"> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.089</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="four wavelength" wavelength_1="1.4013" wavelength_2="1.3852"> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.086</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="four wavelength" wavelength_1="1.4013" wavelength_2="1.3847"> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.077</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="four wavelength" wavelength_1="1.3857" wavelength_2="1.3857"> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:ratio_one_wl>0.140</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.127</PDBx:ratio_one_wl_centric> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="four wavelength" wavelength_1="1.3857" wavelength_2="1.3852"> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.085</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="four wavelength" wavelength_1="1.3857" wavelength_2="1.3847"> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.089</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="four wavelength" wavelength_1="1.3852" wavelength_2="1.3852"> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:ratio_one_wl>0.155</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.119</PDBx:ratio_one_wl_centric> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="four wavelength" wavelength_1="1.3852" wavelength_2="1.3847"> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.082</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="four wavelength" wavelength_1="1.3847" wavelength_2="1.3847"> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:ratio_one_wl>0.124</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.120</PDBx:ratio_one_wl_centric> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="five wavelength" wavelength_1="1.3857" wavelength_2="1.3857"> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:ratio_one_wl>0.075</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.027</PDBx:ratio_one_wl_centric> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="five wavelength" wavelength_1="1.3857" wavelength_2="1.3852"> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.041</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="five wavelength" wavelength_1="1.3857" wavelength_2="1.3847"> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.060</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="five wavelength" wavelength_1="1.3857" wavelength_2="1.3784"> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.057</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="five wavelength" wavelength_1="1.3857" wavelength_2="1.2862"> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.072</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="five wavelength" wavelength_1="1.3852" wavelength_2="1.3852"> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:ratio_one_wl>0.105</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.032</PDBx:ratio_one_wl_centric> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="five wavelength" wavelength_1="1.3852" wavelength_2="1.3847"> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.036</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="five wavelength" wavelength_1="1.3852" wavelength_2="1.3784"> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.044</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="five wavelength" wavelength_1="1.3852" wavelength_2="1.2862"> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.065</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="five wavelength" wavelength_1="1.3847" wavelength_2="1.3847"> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:ratio_one_wl>0.072</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.031</PDBx:ratio_one_wl_centric> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="five wavelength" wavelength_1="1.3847" wavelength_2="1.3784"> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.040</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="five wavelength" wavelength_1="1.3847" wavelength_2="1.2862"> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.059</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="five wavelength" wavelength_1="1.3784" wavelength_2="1.3784"> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:ratio_one_wl>0.059</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.032</PDBx:ratio_one_wl_centric> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="five wavelength" wavelength_1="1.3784" wavelength_2="1.2862"> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.059</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="five wavelength" wavelength_1="1.2862" wavelength_2="1.3847"> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:ratio_one_wl>0.058</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.028</PDBx:ratio_one_wl_centric> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="five wavelength" wavelength_1="1.3857" wavelength_2="1.3857"> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:ratio_one_wl>0.078</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.075</PDBx:ratio_one_wl_centric> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="five wavelength" wavelength_1="1.3857" wavelength_2="1.3852"> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.059</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="five wavelength" wavelength_1="1.3857" wavelength_2="1.3847"> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.067</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="five wavelength" wavelength_1="1.3857" wavelength_2="1.3784"> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.084</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="five wavelength" wavelength_1="1.3857" wavelength_2="1.2862"> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.073</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="five wavelength" wavelength_1="1.3852" wavelength_2="1.3852"> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:ratio_one_wl>0.101</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.088</PDBx:ratio_one_wl_centric> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="five wavelength" wavelength_1="1.3852" wavelength_2="1.3847"> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.066</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="five wavelength" wavelength_1="1.3852" wavelength_2="1.3784"> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.082</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="five wavelength" wavelength_1="1.3852" wavelength_2="1.2862"> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.085</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="five wavelength" wavelength_1="1.3847" wavelength_2="1.3847"> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:ratio_one_wl>0.097</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.074</PDBx:ratio_one_wl_centric> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="five wavelength" wavelength_1="1.3847" wavelength_2="1.3784"> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.081</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="five wavelength" wavelength_1="1.3847" wavelength_2="1.2862"> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.085</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="five wavelength" wavelength_1="1.3784" wavelength_2="1.3784"> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:ratio_one_wl>0.114</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.089</PDBx:ratio_one_wl_centric> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="five wavelength" wavelength_1="1.3784" wavelength_2="1.2862"> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.103</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="1" clust_id="five wavelength" wavelength_1="1.2862" wavelength_2="1.2862"> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:ratio_one_wl>0.062</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.060</PDBx:ratio_one_wl_centric> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="2" clust_id="five wavelength" wavelength_1="0.7263" wavelength_2="0.7263"> <PDBx:d_res_low>15.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:ratio_one_wl>0.035</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.026</PDBx:ratio_one_wl_centric> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="2" clust_id="five wavelength" wavelength_1="0.7263" wavelength_2="0.7251"> <PDBx:d_res_low>15.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.028</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="2" clust_id="five wavelength" wavelength_1="0.7263" wavelength_2="0.7284"> <PDBx:d_res_low>15.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.023</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="2" clust_id="five wavelength" wavelength_1="0.7263" wavelength_2="0.7246"> <PDBx:d_res_low>15.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.025</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="2" clust_id="five wavelength" wavelength_1="0.7263" wavelength_2="0.7217"> <PDBx:d_res_low>15.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.026</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="2" clust_id="five wavelength" wavelength_1="0.7251" wavelength_2="0.7251"> <PDBx:d_res_low>15.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:ratio_one_wl>0.060</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.026</PDBx:ratio_one_wl_centric> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="2" clust_id="five wavelength" wavelength_1="0.7251" wavelength_2="0.7284"> <PDBx:d_res_low>15.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.029</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="2" clust_id="five wavelength" wavelength_1="0.7251" wavelength_2="0.7246"> <PDBx:d_res_low>15.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.031</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="2" clust_id="five wavelength" wavelength_1="0.7251" wavelength_2="0.7217"> <PDBx:d_res_low>15.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.035</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="2" clust_id="five wavelength" wavelength_1="0.7284" wavelength_2="0.7284"> <PDBx:d_res_low>15.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:ratio_one_wl>0.075</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.030</PDBx:ratio_one_wl_centric> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="2" clust_id="five wavelength" wavelength_1="0.7284" wavelength_2="0.7246"> <PDBx:d_res_low>15.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.023</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="2" clust_id="five wavelength" wavelength_1="0.7284" wavelength_2="0.7217"> <PDBx:d_res_low>15.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.027</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="2" clust_id="five wavelength" wavelength_1="0.7246" wavelength_2="0.7246"> <PDBx:d_res_low>15.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:ratio_one_wl>0.069</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.026</PDBx:ratio_one_wl_centric> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="2" clust_id="five wavelength" wavelength_1="0.7246" wavelength_2="0.7217"> <PDBx:d_res_low>15.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:ratio_two_wl>0.024</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="2" clust_id="five wavelength" wavelength_1="0.7217" wavelength_2="0.7284"> <PDBx:d_res_low>15.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:ratio_one_wl>0.060</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.028</PDBx:ratio_one_wl_centric> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="2" clust_id="five wavelength" wavelength_1="0.7263" wavelength_2="0.7263"> <PDBx:d_res_low>3.00</PDBx:d_res_low> <PDBx:d_res_high>1.90</PDBx:d_res_high> <PDBx:ratio_one_wl>0.060</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.050</PDBx:ratio_one_wl_centric> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="2" clust_id="five wavelength" wavelength_1="0.7263" wavelength_2="0.7251"> <PDBx:d_res_low>3.00</PDBx:d_res_low> <PDBx:d_res_high>1.90</PDBx:d_res_high> <PDBx:ratio_two_wl>0.056</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="2" clust_id="five wavelength" wavelength_1="0.7263" wavelength_2="0.7284"> <PDBx:d_res_low>3.00</PDBx:d_res_low> <PDBx:d_res_high>1.90</PDBx:d_res_high> <PDBx:ratio_two_wl>0.055</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="2" clust_id="five wavelength" wavelength_1="0.7263" wavelength_2="0.7246"> <PDBx:d_res_low>3.00</PDBx:d_res_low> <PDBx:d_res_high>1.90</PDBx:d_res_high> <PDBx:ratio_two_wl>0.053</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="2" clust_id="five wavelength" wavelength_1="0.7263" wavelength_2="0.7217"> <PDBx:d_res_low>3.00</PDBx:d_res_low> <PDBx:d_res_high>1.90</PDBx:d_res_high> <PDBx:ratio_two_wl>0.056</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="2" clust_id="five wavelength" wavelength_1="0.7251" wavelength_2="0.7251"> <PDBx:d_res_low>3.00</PDBx:d_res_low> <PDBx:d_res_high>1.90</PDBx:d_res_high> <PDBx:ratio_one_wl>0.089</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.050</PDBx:ratio_one_wl_centric> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="2" clust_id="five wavelength" wavelength_1="0.7251" wavelength_2="0.7284"> <PDBx:d_res_low>3.00</PDBx:d_res_low> <PDBx:d_res_high>1.90</PDBx:d_res_high> <PDBx:ratio_two_wl>0.054</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="2" clust_id="five wavelength" wavelength_1="0.7251" wavelength_2="0.7246"> <PDBx:d_res_low>3.00</PDBx:d_res_low> <PDBx:d_res_high>1.90</PDBx:d_res_high> <PDBx:ratio_two_wl>0.058</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="2" clust_id="five wavelength" wavelength_1="0.7251" wavelength_2="0.7217"> <PDBx:d_res_low>3.00</PDBx:d_res_low> <PDBx:d_res_high>1.90</PDBx:d_res_high> <PDBx:ratio_two_wl>0.063</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="2" clust_id="five wavelength" wavelength_1="0.7284" wavelength_2="0.7284"> <PDBx:d_res_low>3.00</PDBx:d_res_low> <PDBx:d_res_high>1.90</PDBx:d_res_high> <PDBx:ratio_one_wl>0.104</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.057</PDBx:ratio_one_wl_centric> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="2" clust_id="five wavelength" wavelength_1="0.7284" wavelength_2="0.7246"> <PDBx:d_res_low>3.00</PDBx:d_res_low> <PDBx:d_res_high>1.90</PDBx:d_res_high> <PDBx:ratio_two_wl>0.052</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="2" clust_id="five wavelength" wavelength_1="0.7284" wavelength_2="0.7217"> <PDBx:d_res_low>3.00</PDBx:d_res_low> <PDBx:d_res_high>1.90</PDBx:d_res_high> <PDBx:ratio_two_wl>0.057</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="2" clust_id="five wavelength" wavelength_1="0.7246" wavelength_2="0.7246"> <PDBx:d_res_low>3.00</PDBx:d_res_low> <PDBx:d_res_high>1.90</PDBx:d_res_high> <PDBx:ratio_one_wl>0.098</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.052</PDBx:ratio_one_wl_centric> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="2" clust_id="five wavelength" wavelength_1="0.7246" wavelength_2="0.7217"> <PDBx:d_res_low>3.00</PDBx:d_res_low> <PDBx:d_res_high>1.90</PDBx:d_res_high> <PDBx:ratio_two_wl>0.054</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio expt_id="2" clust_id="five wavelength" wavelength_1="0.7217" wavelength_2="0.7284"> <PDBx:d_res_low>3.00</PDBx:d_res_low> <PDBx:d_res_high>1.90</PDBx:d_res_high> <PDBx:ratio_one_wl>0.089</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.060</PDBx:ratio_one_wl_centric> </PDBx:phasing_MAD_ratio> </PDBx:phasing_MAD_ratioCategory> The highest resolution for the interplanar spacing in the reflection data used for this comparison of Bijvoet differences. This is the smallest d value. The lowest resolution for the interplanar spacing in the reflection data used for this comparison of Bijvoet differences. This is the largest d value. The root mean square Bijvoet difference at one wavelength for all reflections. The root mean square Bijvoet difference at one wavelength for centric reflections. This would be equal to zero for perfect data, and thus serves as an estimate of the noise in the anomalous signals. The root mean square dispersive Bijvoet difference between two wavelengths for all reflections. This data item is a pointer to attribute id in category phasing_MAD_clust in the PHASING_MAD_CLUST category. This data item is a pointer to attribute id in category phasing_MAD_expt in the PHASING_MAD_EXPT category. This data item is a pointer to attribute wavelength in category phasing_MAD_set in the PHASING_MAD_SET category. This data item is a pointer to attribute wavelength in category phasing_MAD_set in the PHASING_MAD_SET category. Data items in the PHASING_MAD_SET category record details about the individual data sets used in a MAD phasing experiment. Example 1 - based on a paper by Shapiro et al. [(1995). Nature (London), 374, 327-337] <PDBx:phasing_MAD_setCategory> <PDBx:phasing_MAD_set expt_id="1" clust_id="four wavelength" set_id="aa" wavelength="1.4013"> <PDBx:wavelength_details>pre-edge</PDBx:wavelength_details> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:f_prime>-12.48</PDBx:f_prime> <PDBx:f_double_prime>3.80</PDBx:f_double_prime> </PDBx:phasing_MAD_set> <PDBx:phasing_MAD_set expt_id="1" clust_id="four wavelength" set_id="bb" wavelength="1.3857"> <PDBx:wavelength_details>peak</PDBx:wavelength_details> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:f_prime>-31.22</PDBx:f_prime> <PDBx:f_double_prime>17.20</PDBx:f_double_prime> </PDBx:phasing_MAD_set> <PDBx:phasing_MAD_set expt_id="1" clust_id="four wavelength" set_id="cc" wavelength="1.3852"> <PDBx:wavelength_details>edge</PDBx:wavelength_details> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:f_prime>-13.97</PDBx:f_prime> <PDBx:f_double_prime>29.17</PDBx:f_double_prime> </PDBx:phasing_MAD_set> <PDBx:phasing_MAD_set expt_id="1" clust_id="four wavelength" set_id="dd" wavelength="1.3847"> <PDBx:wavelength_details>remote</PDBx:wavelength_details> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:f_prime>-6.67</PDBx:f_prime> <PDBx:f_double_prime>17.34</PDBx:f_double_prime> </PDBx:phasing_MAD_set> <PDBx:phasing_MAD_set expt_id="1" clust_id="five wavelength" set_id="ee" wavelength="1.3857"> <PDBx:wavelength_details>ascending edge</PDBx:wavelength_details> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:f_prime>-28.33</PDBx:f_prime> <PDBx:f_double_prime>14.84</PDBx:f_double_prime> </PDBx:phasing_MAD_set> <PDBx:phasing_MAD_set expt_id="1" clust_id="five wavelength" set_id="ff" wavelength="1.3852"> <PDBx:wavelength_details>peak</PDBx:wavelength_details> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:f_prime>-21.50</PDBx:f_prime> <PDBx:f_double_prime>30.23</PDBx:f_double_prime> </PDBx:phasing_MAD_set> <PDBx:phasing_MAD_set expt_id="1" clust_id="five wavelength" set_id="gg" wavelength="1.3847"> <PDBx:wavelength_details>descending edge</PDBx:wavelength_details> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:f_prime>-10.71</PDBx:f_prime> <PDBx:f_double_prime>20.35</PDBx:f_double_prime> </PDBx:phasing_MAD_set> <PDBx:phasing_MAD_set expt_id="1" clust_id="five wavelength" set_id="hh" wavelength="1.3784"> <PDBx:wavelength_details>remote 1</PDBx:wavelength_details> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:f_prime>-14.45</PDBx:f_prime> <PDBx:f_double_prime>11.84</PDBx:f_double_prime> </PDBx:phasing_MAD_set> <PDBx:phasing_MAD_set expt_id="1" clust_id="five wavelength" set_id="ii" wavelength="1.2862"> <PDBx:wavelength_details>remote 2</PDBx:wavelength_details> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:f_prime>-9.03</PDBx:f_prime> <PDBx:f_double_prime>9.01</PDBx:f_double_prime> </PDBx:phasing_MAD_set> <PDBx:phasing_MAD_set expt_id="2" clust_id="five wavelength" set_id="jj" wavelength="0.7263"> <PDBx:wavelength_details>pre-edge</PDBx:wavelength_details> <PDBx:d_res_low>15.00</PDBx:d_res_low> <PDBx:d_res_high>1.90</PDBx:d_res_high> <PDBx:f_prime>-21.10</PDBx:f_prime> <PDBx:f_double_prime>4.08</PDBx:f_double_prime> </PDBx:phasing_MAD_set> <PDBx:phasing_MAD_set expt_id="2" clust_id="five wavelength" set_id="kk" wavelength="0.7251"> <PDBx:wavelength_details>edge</PDBx:wavelength_details> <PDBx:d_res_low>15.00</PDBx:d_res_low> <PDBx:d_res_high>1.90</PDBx:d_res_high> <PDBx:f_prime>-34.72</PDBx:f_prime> <PDBx:f_double_prime>7.92</PDBx:f_double_prime> </PDBx:phasing_MAD_set> <PDBx:phasing_MAD_set expt_id="2" clust_id="five wavelength" set_id="ll" wavelength="0.7248"> <PDBx:wavelength_details>peak</PDBx:wavelength_details> <PDBx:d_res_low>15.00</PDBx:d_res_low> <PDBx:d_res_high>1.90</PDBx:d_res_high> <PDBx:f_prime>-24.87</PDBx:f_prime> <PDBx:f_double_prime>10.30</PDBx:f_double_prime> </PDBx:phasing_MAD_set> <PDBx:phasing_MAD_set expt_id="2" clust_id="five wavelength" set_id="mm" wavelength="0.7246"> <PDBx:wavelength_details>descending edge</PDBx:wavelength_details> <PDBx:d_res_low>15.00</PDBx:d_res_low> <PDBx:d_res_high>1.90</PDBx:d_res_high> <PDBx:f_prime>-17.43</PDBx:f_prime> <PDBx:f_double_prime>9.62</PDBx:f_double_prime> </PDBx:phasing_MAD_set> <PDBx:phasing_MAD_set expt_id="2" clust_id="five wavelength" set_id="nn" wavelength="0.7217"> <PDBx:wavelength_details>remote</PDBx:wavelength_details> <PDBx:d_res_low>15.00</PDBx:d_res_low> <PDBx:d_res_high>1.90</PDBx:d_res_high> <PDBx:f_prime>-13.26</PDBx:f_prime> <PDBx:f_double_prime>8.40</PDBx:f_double_prime> </PDBx:phasing_MAD_set> </PDBx:phasing_MAD_setCategory> The highest resolution for the interplanar spacing in the reflection data used for this set of data. This is the smallest d value. The lowest resolution for the interplanar spacing in the reflection data used for this set of data. This is the largest d value. The f'' component of the anomalous scattering factor for this wavelength. The f' component of the anomalous scattering factor for this wavelength. record the type of heavy atoms which produce anomolous singal. record the refined f_double_prime (not from experiment). record the refined f_prime (not from experiment). A descriptor for this wavelength in this cluster of data sets. peak remote ascending edge This data item is a pointer to attribute id in category phasing_MAD_expt in the PHASING_MAD_EXPT category. This data item is a pointer to attribute id in category phasing_MAD_clust in the PHASING_MAD_CLUST category. This data item is a pointer to attribute id in category phasing_set in the PHASING_SET category. The wavelength at which this data set was measured. Data items in the PHASING_MIR category record details about the phasing of the structure, when methods involving isomorphous replacement are involved. All isomorphous based techniques are subsumed in this category, including single isomorphous replacement (SIR), multiple isomorphous replacement (MIR), single or multiple isomorphous replacement plus anomalous scattering (SIRAS, MIRAS). Example 1 - based on a paper by Zanotti et al. [(1993). J. Biol. Chem. 268, 10728-10738]. <PDBx:phasing_MIRCategory> <PDBx:phasing_MIR> <PDBx:method> Standard phase refinement (Blow &amp; Crick, 1959)</PDBx:method> </PDBx:phasing_MIR> </PDBx:phasing_MIRCategory> The mean value of the figure of merit m for all reflections phased in the native data set. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~a~ = the probability that phase angle a is correct the integral is taken over the range alpha = 0 to 2 pi. The mean value of the figure of merit m for the acentric reflections phased in the native data set. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~a~ = the probability that phase angle a is correct the integral is taken over the range alpha = 0 to 2 pi. The mean value of the figure of merit m for the centric reflections phased in the native data set. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~a~ = the probability that phase angle a is correct the integral is taken over the range alpha = 0 to 2 pi. The highest resolution in angstroms for the interplanar spacing in the reflection data used for the native data set. This is the smallest d value. The lowest resolution in angstroms for the interplanar spacing in the reflection data used for the native data set. This is the largest d value. A description of special aspects of the isomorphous phasing. A description of the MIR phasing method applied to phase this structure. Note that this is not the computer program used, which is described in the SOFTWARE category, but rather the method itself. This data item should be used to describe significant methodological options used within the MIR phasing program. The total number of reflections phased in the native data set. The number of acentric reflections phased in the native data set. The number of centric reflections phased in the native data set. Criterion used to limit the reflections used in the phasing calculations. > 4 \s(I) This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the PHASING_MIR_DER category record details about individual derivatives used in the phasing of the structure when methods involving isomorphous replacement are involved. A derivative in this context does not necessarily equate with a data set; for instance, the same data set could be used to one resolution limit as an isomorphous scatterer and to a different resolution (and with a different sigma cutoff) as an anomalous scatterer. These would be treated as two distinct derivatives, although both derivatives would point to the same data sets via attribute der_set_id in category phasing_MIR_der and attribute native_set_id in category phasing_MIR_der. Example 1 - based on a paper by Zanotti et al. [(1993). J. Biol. Chem. 268, 10728-10738]. <PDBx:phasing_MIR_derCategory> <PDBx:phasing_MIR_der id="KAu(CN)2"> <PDBx:number_of_sites>3</PDBx:number_of_sites> <PDBx:details>major site interpreted in difference Patterson</PDBx:details> </PDBx:phasing_MIR_der> <PDBx:phasing_MIR_der id="K2HgI4"> <PDBx:number_of_sites>6</PDBx:number_of_sites> <PDBx:details>sites found in cross-difference Fourier</PDBx:details> </PDBx:phasing_MIR_der> <PDBx:phasing_MIR_der id="K3IrCl6"> <PDBx:number_of_sites>2</PDBx:number_of_sites> <PDBx:details>sites found in cross-difference Fourier</PDBx:details> </PDBx:phasing_MIR_der> <PDBx:phasing_MIR_der id="All"> <PDBx:number_of_sites>11</PDBx:number_of_sites> <PDBx:details>data for all three derivatives combined</PDBx:details> </PDBx:phasing_MIR_der> </PDBx:phasing_MIR_derCategory> Residual factor R~cullis,acen~ for acentric reflections in this derivative. The Cullis R factor was originally defined only for centric reflections. It is, however, also a useful statistical measure for acentric reflections, which is how it is used in this data item. sum| |Fph~obs~ +/- Fp~obs~| - Fh~calc~ | R~cullis,acen~ = ---------------------------------------- sum|Fph~obs~ - Fp~obs~| Fp~obs~ = the observed structure factor amplitude of the native Fph~obs~ = the observed structure factor amplitude of the derivative Fh~calc~ = the calculated structure factor amplitude from the heavy atom model sum is taken over the specified reflections Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G. & North, A. C. T. (1961). Proc. Roy. Soc. A265, 15-38. Residual factor R~cullis,ano~ for anomalous reflections in this derivative. The Cullis R factor was originally defined only for centric reflections. It is, however, also a useful statistical measure for anomalous reflections, which is how it is used in this data item. This is tabulated for acentric terms. Any value <1.0 means there is some contribution to the phasing from the anomalous data. sum| |Fph+~obs~Fph-~obs~ - Fh+~calc~ - Fh-~calc~| | R~cullis,ano~ = --------------------------------------------------- sum|Fph+~obs~ - Fph-~obs~| Fph+~obs~ = the observed positive Friedel structure factor amplitude for the derivative Fph-~obs~ = the observed negative Friedel structure factor amplitude for the derivative Fh+~calc~ = the calculated positive Friedel structure factor amplitude from the heavy atom model Fh-~calc~ = the calculated negative Friedel structure factor amplitude from the heavy atom model sum is taken over the specified reflections Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G. & North, A. C. T. (1961). Proc. Roy. Soc. A265, 15-38. Residual factor R~cullis~ for centric reflections in this derivative. sum| |Fph~obs~ +/- Fp~obs~| - Fh~calc~ | R~cullis~ = ---------------------------------------- sum|Fph~obs~ - Fp~obs~| Fp~obs~ = the observed structure factor amplitude of the native Fph~obs~ = the observed structure factor amplitude of the derivative Fh~calc~ = the calculated structure factor amplitude from the heavy atom model sum is taken over the specified reflections Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G. & North, A. C. T. (1961). Proc. Roy. Soc. A265, 15-38. The highest resolution for the interplanar spacing in the reflection data used for this derivative. This is the smallest d value. The lowest resolution for the interplanar spacing in the reflection data used for this derivative. This is the highest d value. The data set that was treated as the derivative in this experiment. This data item is a pointer to attribute id in category phasing_set in the PHASING_SET category. A description of special aspects of this derivative, its data, its solution, or its use in phasing. The data set that was treated as the native in this experiment. This data item is a pointer to attribute id in category phasing_set in the PHASING_SET category. The number of heavy atom sites in this derivative. record R_cullis for each derivative. record R_kraut obtained from all data data for each derivative. record R_kraut obtained from acentric data for each derivative. record R_kraut obtained from centric data for each derivative. record figure of merit obtained from all data for each derivative. record figure of merit obtained from acentric data for each derivative. record figure of merit obtained from centric data for each derivative. record lack of closure obtained from all data for each derivative. record lack of closure obtained from acentric data for each derivative. record lack of closure obtained from centric data for each derivative. record phasing power for each derivative. record number of reflections used for each derivative. The mean phasing power P for acentric reflections in this derivative. sum|Fh~calc~^2^| P = (----------------------------)^1/2^ sum|Fph~obs~ - Fph~calc~|^2^ Fph~obs~ = the observed structure factor amplitude of this derivative Fph~calc~ = the calculated structure factor amplitude of this derivative Fh~calc~ = the calculated structure factor amplitude from the heavy atom model sum is taken over the specified reflections The mean phasing power P for centric reflections in this derivative. sum|Fh~calc~^2^| P = (----------------------------)^1/2^ sum|Fph~obs~ - Fph~calc~|^2^ Fph~obs~ = the observed structure factor amplitude of the derivative Fph~calc~ = the calculated structure factor amplitude of the derivative Fh~calc~ = the calculated structure factor amplitude from the heavy atom model sum is taken over the specified reflections The number of acentric reflections used in phasing for this derivative. The number of anomalous reflections used in phasing for this derivative. The number of centric reflections used in phasing for this derivative. Criteria used to limit the reflections used in the phasing calculations. > 4 \s(I) The value of attribute id in category phasing_MIR_der must uniquely identify a record in the PHASING_MIR_DER list. Note that this item need not be a number; it can be any unique identifier. KAu(CN)2 K2HgI4_anom K2HgI4_iso Data items in the PHASING_MIR_DER_REFLN category record details about the calculated structure factors obtained in an MIR phasing experiment. This list may contain information from a number of different derivatives; attribute der_id in category phasing_MIR_der_refln indicates to which derivative a given record corresponds. (A derivative in this context does not necessarily equate with a data set; see the definition of the PHASING_MIR_DER category for a more thorough discussion of the meaning of derivative.) It is not necessary for the data items describing the measured value of F to appear in this list, as they will already have been given in the PHASING_SET_REFLN category. However, these items may also be listed here for completeness, if desired. Example 1 - based on laboratory records for the (6,1,25) reflection obtained for a Hg/Pt derivative of protein NS1. <PDBx:phasing_MIR_der_reflnCategory> <PDBx:phasing_MIR_der_refln index_h="6" index_k="1" index_l="25" der_id="HGPT1" set_id="NS1-96"> <PDBx:F_calc_au>106.66</PDBx:F_calc_au> <PDBx:F_meas_au>204.67</PDBx:F_meas_au> <PDBx:F_meas_sigma>6.21</PDBx:F_meas_sigma> <PDBx:HL_A_iso>-3.15</PDBx:HL_A_iso> <PDBx:HL_B_iso>-0.76</PDBx:HL_B_iso> <PDBx:HL_C_iso>0.65</PDBx:HL_C_iso> <PDBx:HL_D_iso>0.23</PDBx:HL_D_iso> <PDBx:phase_calc>194.48</PDBx:phase_calc> </PDBx:phasing_MIR_der_refln> </PDBx:phasing_MIR_der_reflnCategory> The calculated value of the structure factor for this derivative, in electrons. The calculated value of the structure factor for this derivative, in arbitrary units. The measured value of the structure factor for this derivative, in electrons. The measured value of the structure factor for this derivative, in arbitrary units. The estimated standard deviation of attribute F_meas in category phasing_MIR_der_refln in electrons. The estimated standard deviation of attribute F_meas_au in category phasing_MIR_der_refln in arbitrary units. The isomorphous Hendrickson-Lattman coefficient A~iso~ for this reflection for this derivative. -2.0 * (Fp~obs~^2^ + Fh~calc~^2^ - Fph~obs~^2^) * Fp~obs~ * cos(alphah~calc~) A~iso~ = ----------------------------------------------- E^2^ E = (Fph~obs~ - Fp~obs~ - Fh~calc~)^2^ for centric reflections = [(Fph~obs~ - Fp~obs~) * 2^1/2^ - Fh~calc~]^2^ for acentric reflections Fp~obs~ = the observed structure factor amplitude of the native Fph~obs~ = the observed structure factor amplitude of the derivative Fh~calc~ = the calculated structure factor amplitude from the heavy atom model alphah~calc~ = the calculated phase from the heavy atom model The isomorphous Hendrickson-Lattman coefficient B~iso~ for this reflection for this derivative. -2.0 * (Fp~obs~^2^ + Fh~calc~^2^ - Fph~obs~^2^) * Fp~obs~ * sin(alphah~calc~) B~iso~ = ----------------------------------------------- E^2^ E = (Fph~obs~ - Fp~obs~ - Fh~calc~)^2^ for centric reflections = [(Fph~obs~ - Fp~obs~) * 2^1/2^ - Fh~calc~]^2^ for acentric reflections Fp~obs~ = the observed structure factor amplitude of the native Fph~obs~ = the observed structure factor amplitude of the derivative Fh~calc~ = the calculated structure factor amplitude from the heavy atom model alphah~calc~ = the phase calculated from the heavy atom model The isomorphous Hendrickson-Lattman coefficient C~iso~ for this reflection for this derivative. -Fp~obs~^2^ * [sin(alphah~calc~)^2^ - cos(alphah~calc~)^2^] C~iso~ = ------------------------------------ E^2^ E = (Fph~obs~ - Fp~obs~ - Fh~calc~)^2^ for centric reflections = [(Fph~obs~ - Fp~obs~) * 2^1/2^ - Fh~calc~]^2^ for acentric reflections Fp~obs~ = the observed structure factor amplitude of the native Fph~obs~ = the observed structure factor amplitude of the derivative Fh~calc~ = the calculated structure factor amplitude from the heavy atom model alphah~calc~ = the phase calculated from the heavy atom model The isomorphous Hendrickson-Lattman coefficient D~iso~ for this reflection for this derivative. -2.0 * Fp~obs~^2^ * sin(alphah~calc~)^2^ * cos(alphah~calc~)^2^ D~iso~ = ---------------------------------------- E^2^ E = (Fph~obs~ - Fp~obs~ - Fh~calc~)^2^ for centric reflections = [(Fph~obs~ - Fp~obs~) * 2^1/2^ - Fh~calc~]^2^ for acentric reflections Fp~obs~ = the observed structure factor amplitude of the native Fph~obs~ = the observed structure factor amplitude of the derivative Fh~calc~ = the calculated structure factor amplitude from the heavy atom model alphah~calc~ = the phase calculated from the heavy atom model The calculated value of the structure-factor phase, based on the heavy atom model, for this derivative, in degrees. Miller index h for this reflection for this derivative. Miller index k for this reflection for this derivative. Miller index l for this reflection for this derivative. This data item is a pointer to attribute id in category phasing_MIR_der in the PHASING_MIR_DER category. This data item is a pointer to attribute id in category phasing_set in the PHASING_SET category. Data items in the PHASING_MIR_DER_SHELL category record statistics, broken down into shells of resolution, for an MIR phasing experiment. This list may contain information from a number of different derivatives; attribute der_id in category phasing_MIR_der_shell indicates to which derivative a given record corresponds. (A derivative in this context does not necessarily equate with a data set; see the definition of the PHASING_MIR_DER category for a more thorough discussion of the meaning of derivative.) Example 1 - based on a paper by Zanotti et al. [(1993). J. Biol. Chem. 268, 10728-10738]. with addition of an arbitrary low-resolution limit <PDBx:phasing_MIR_der_shellCategory> <PDBx:phasing_MIR_der_shell der_id="KAu(CN)2" d_res_low="15.0" d_res_high="8.3"> <PDBx:ha_ampl>54</PDBx:ha_ampl> <PDBx:loc>26</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell der_id="KAu(CN)2" d_res_low="8.3" d_res_high="6.4"> <PDBx:ha_ampl>54</PDBx:ha_ampl> <PDBx:loc>20</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell der_id="KAu(CN)2" d_res_low="6.4" d_res_high="5.2"> <PDBx:ha_ampl>50</PDBx:ha_ampl> <PDBx:loc>20</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell der_id="KAu(CN)2" d_res_low="5.2" d_res_high="4.4"> <PDBx:ha_ampl>44</PDBx:ha_ampl> <PDBx:loc>23</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell der_id="KAu(CN)2" d_res_low="4.4" d_res_high="3.8"> <PDBx:ha_ampl>39</PDBx:ha_ampl> <PDBx:loc>23</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell der_id="KAu(CN)2" d_res_low="3.8" d_res_high="3.4"> <PDBx:ha_ampl>33</PDBx:ha_ampl> <PDBx:loc>21</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell der_id="KAu(CN)2" d_res_low="3.4" d_res_high="3.0"> <PDBx:ha_ampl>28</PDBx:ha_ampl> <PDBx:loc>17</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell der_id="KAu(CN)2" d_res_low="15.0" d_res_high="3.0"> <PDBx:ha_ampl>38</PDBx:ha_ampl> <PDBx:loc>21</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell der_id="K2HgI4" d_res_low="15.0" d_res_high="8.3"> <PDBx:ha_ampl>149</PDBx:ha_ampl> <PDBx:loc>87</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell der_id="K2HgI4" d_res_low="8.3" d_res_high="6.4"> <PDBx:ha_ampl>121</PDBx:ha_ampl> <PDBx:loc>73</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell der_id="K2HgI4" d_res_low="6.4" d_res_high="5.2"> <PDBx:ha_ampl>95</PDBx:ha_ampl> <PDBx:loc>61</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell der_id="K2HgI4" d_res_low="5.2" d_res_high="4.4"> <PDBx:ha_ampl>80</PDBx:ha_ampl> <PDBx:loc>60</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell der_id="K2HgI4" d_res_low="4.4" d_res_high="3.8"> <PDBx:ha_ampl>73</PDBx:ha_ampl> <PDBx:loc>63</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell der_id="K2HgI4" d_res_low="3.8" d_res_high="3.4"> <PDBx:ha_ampl>68</PDBx:ha_ampl> <PDBx:loc>57</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell der_id="K2HgI4" d_res_low="3.4" d_res_high="3.0"> <PDBx:ha_ampl>63</PDBx:ha_ampl> <PDBx:loc>46</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell der_id="K2HgI4" d_res_low="15.0" d_res_high="3.0"> <PDBx:ha_ampl>79</PDBx:ha_ampl> <PDBx:loc>58</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell der_id="K3IrCl6" d_res_low="15.0" d_res_high="8.3"> <PDBx:ha_ampl>33</PDBx:ha_ampl> <PDBx:loc>27</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell der_id="K3IrCl6" d_res_low="8.3" d_res_high="6.4"> <PDBx:ha_ampl>40</PDBx:ha_ampl> <PDBx:loc>23</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell der_id="K3IrCl6" d_res_low="6.4" d_res_high="5.2"> <PDBx:ha_ampl>31</PDBx:ha_ampl> <PDBx:loc>22</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell der_id="K3IrCl6" d_res_low="5.2" d_res_high="4.4"> <PDBx:ha_ampl>27</PDBx:ha_ampl> <PDBx:loc>23</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell der_id="K3IrCl6" d_res_low="4.4" d_res_high="3.8"> <PDBx:ha_ampl>22</PDBx:ha_ampl> <PDBx:loc>23</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell der_id="K3IrCl6" d_res_low="3.8" d_res_high="3.4"> <PDBx:ha_ampl>19</PDBx:ha_ampl> <PDBx:loc>20</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell der_id="K3IrCl6" d_res_low="3.4" d_res_high="3.0"> <PDBx:ha_ampl>16</PDBx:ha_ampl> <PDBx:loc>20</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell der_id="K3IrCl6" d_res_low="15.0" d_res_high="3.0"> <PDBx:ha_ampl>23</PDBx:ha_ampl> <PDBx:loc>21</PDBx:loc> </PDBx:phasing_MIR_der_shell> </PDBx:phasing_MIR_der_shellCategory> Residual factor R~cullis~ for centric reflections in this derivative in this shell. sum| |Fph~obs~ +/- Fp~obs~| - Fh~calc~ | R~cullis~ = ---------------------------------------- sum|Fph~obs~ - Fp~obs~| Fp~obs~ = the observed structure factor amplitude of the native Fph~obs~ = the observed structure factor amplitude of the derivative Fh~calc~ = the calculated structure factor amplitude from the heavy atom model sum is taken over the specified reflections Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G. & North, A. C. T. (1961). Proc. R. Soc. A265, 15-38. Residual factor R~kraut~ for general reflections in this derivative in this shell. sum|Fph~obs~ - Fph~calc~| R~kraut~ = ------------------------- sum|Fph~obs~| Fph~obs~ = the observed structure factor amplitude of the derivative Fph~calc~ = the calculated structure factor amplitude of the derivative sum is taken over the specified reflections Ref: Kraut, J., Sieker, L. C., High, D. F. & Freer, S. T. (1962). Proc. Natl. Acad. Sci. USA, 48, 1417-14??. The mean value of the figure of merit m for reflections for this derivative in this shell. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~alpha~ = the probability that phase angle alpha is correct int is taken over the range alpha = 0 to 2 pi. The mean heavy-atom amplitude for reflections in this derivative in this shell. The mean lack-of-closure error loc for reflections in this derivative in this shell. loc = sum|Fph~obs~ - Fph~calc~| Fph~obs~ = the observed structure factor amplitude of the derivative Fph~calc~ = the calculated structure factor amplitude of the derivative sum is taken over the specified reflections record R Cullis obtained from acentric data for each derivative, but broken into resolution shells record R Cullis obtained from centric data for each derivative, but broken into resolution shells record R Kraut obtained from acentric data for each derivative, but broken into resolution shells record R Kraut obtained from centric data for each derivative, but broken into resolution shells record figure of merit obtained from acentric data for each derivative, but broken into resolution shells record figure of merit obtained from centric data for each derivative, but broken into resolution shells record lack of closure obtained from acentric data for each derivative, but broken into resolution shells record lack of closure obtained from centric data for each derivative, but broken into resolution shells record phasing power obtained from acentric data for each derivative, but broken into resolution shells record phasing power obtained from centric data for each derivative, but broken into resolution shells record number of acentric reflections used for phasing for each derivative, but broken into resolution shells record number of centric reflections used for phasing for each derivative, but broken into resolution shells The mean of the phase values for reflections in this derivative in this shell. The mean phasing power P for reflections in this derivative in this shell. sum|Fh~calc~^2^| P = (----------------------------)^1/2^ sum|Fph~obs~ - Fph~calc~|^2^ Fph~obs~ = the observed structure factor amplitude of the derivative Fph~calc~ = the calculated structure factor amplitude of the derivative Fh~calc~ = the calculated structure factor amplitude from the heavy atom model sum is taken over the specified reflections The number of reflections in this shell. This data item is a pointer to attribute id in category phasing_MIR_der in the PHASING_MIR_DER category. The lowest resolution for the interplanar spacing in the reflection data for this derivative in this shell. This is the highest d value. The highest resolution for the interplanar spacing in the reflection data for this derivative in this shell. This is the smallest d value. Data items in the PHASING_MIR_DER_SITE category record details about the heavy-atom sites in an MIR phasing experiment. This list may contain information from a number of different derivatives; attribute der_id in category phasing_MIR_der_site indicates to which derivative a given record corresponds. (A derivative in this context does not necessarily equate with a data set; see the definition of the PHASING_MIR_DER category for a more thorough discussion of the meaning of derivative.) Example 1 - based on a paper by Zanotti et al. [(1993). J. Biol. Chem. 268, 10728-10738]. with occupancies converted from electrons to fractional <PDBx:phasing_MIR_der_siteCategory> <PDBx:phasing_MIR_der_site der_id="KAu(CN)2" id="1"> <PDBx:atom_type_symbol>Au</PDBx:atom_type_symbol> <PDBx:occupancy>0.40</PDBx:occupancy> <PDBx:fract_x>0.082</PDBx:fract_x> <PDBx:fract_y>0.266</PDBx:fract_y> <PDBx:fract_z>0.615</PDBx:fract_z> <PDBx:B_iso>33.0</PDBx:B_iso> </PDBx:phasing_MIR_der_site> <PDBx:phasing_MIR_der_site der_id="KAu(CN)2" id="2"> <PDBx:atom_type_symbol>Au</PDBx:atom_type_symbol> <PDBx:occupancy>0.03</PDBx:occupancy> <PDBx:fract_x>0.607</PDBx:fract_x> <PDBx:fract_y>0.217</PDBx:fract_y> <PDBx:fract_z>0.816</PDBx:fract_z> <PDBx:B_iso>25.9</PDBx:B_iso> </PDBx:phasing_MIR_der_site> <PDBx:phasing_MIR_der_site der_id="KAu(CN)2" id="3"> <PDBx:atom_type_symbol>Au</PDBx:atom_type_symbol> <PDBx:occupancy>0.02</PDBx:occupancy> <PDBx:fract_x>0.263</PDBx:fract_x> <PDBx:fract_y>0.782</PDBx:fract_y> <PDBx:fract_z>0.906</PDBx:fract_z> <PDBx:B_iso>15.7</PDBx:B_iso> </PDBx:phasing_MIR_der_site> <PDBx:phasing_MIR_der_site der_id="K2HgI4" id="1"> <PDBx:atom_type_symbol>Hg</PDBx:atom_type_symbol> <PDBx:occupancy>0.63</PDBx:occupancy> <PDBx:fract_x>0.048</PDBx:fract_x> <PDBx:fract_y>0.286</PDBx:fract_y> <PDBx:fract_z>0.636</PDBx:fract_z> <PDBx:B_iso>33.7</PDBx:B_iso> </PDBx:phasing_MIR_der_site> <PDBx:phasing_MIR_der_site der_id="K2HgI4" id="2"> <PDBx:atom_type_symbol>Hg</PDBx:atom_type_symbol> <PDBx:occupancy>0.34</PDBx:occupancy> <PDBx:fract_x>0.913</PDBx:fract_x> <PDBx:fract_y>0.768</PDBx:fract_y> <PDBx:fract_z>0.889</PDBx:fract_z> <PDBx:B_iso>36.7</PDBx:B_iso> </PDBx:phasing_MIR_der_site> <PDBx:phasing_MIR_der_site der_id="K2HgI4" id="3"> <PDBx:atom_type_symbol>Hg</PDBx:atom_type_symbol> <PDBx:occupancy>0.23</PDBx:occupancy> <PDBx:fract_x>0.974</PDBx:fract_x> <PDBx:fract_y>0.455</PDBx:fract_y> <PDBx:fract_z>0.974</PDBx:fract_z> <PDBx:B_iso>24.2</PDBx:B_iso> </PDBx:phasing_MIR_der_site> <PDBx:phasing_MIR_der_site der_id="K2HgI4" id="4"> <PDBx:atom_type_symbol>Hg</PDBx:atom_type_symbol> <PDBx:occupancy>0.28</PDBx:occupancy> <PDBx:fract_x>0.903</PDBx:fract_x> <PDBx:fract_y>0.836</PDBx:fract_y> <PDBx:fract_z>0.859</PDBx:fract_z> <PDBx:B_iso>14.7</PDBx:B_iso> </PDBx:phasing_MIR_der_site> <PDBx:phasing_MIR_der_site der_id="K2HgI4" id="5"> <PDBx:atom_type_symbol>Hg</PDBx:atom_type_symbol> <PDBx:occupancy>0.07</PDBx:occupancy> <PDBx:fract_x>0.489</PDBx:fract_x> <PDBx:fract_y>0.200</PDBx:fract_y> <PDBx:fract_z>0.885</PDBx:fract_z> <PDBx:B_iso>6.4</PDBx:B_iso> </PDBx:phasing_MIR_der_site> <PDBx:phasing_MIR_der_site der_id="K2HgI4" id="6"> <PDBx:atom_type_symbol>Hg</PDBx:atom_type_symbol> <PDBx:occupancy>0.07</PDBx:occupancy> <PDBx:fract_x>0.162</PDBx:fract_x> <PDBx:fract_y>0.799</PDBx:fract_y> <PDBx:fract_z>0.889</PDBx:fract_z> <PDBx:B_iso>32.9</PDBx:B_iso> </PDBx:phasing_MIR_der_site> <PDBx:phasing_MIR_der_site der_id="K3IrCl6" id="1"> <PDBx:atom_type_symbol>Ir</PDBx:atom_type_symbol> <PDBx:occupancy>0.26</PDBx:occupancy> <PDBx:fract_x>0.209</PDBx:fract_x> <PDBx:fract_y>0.739</PDBx:fract_y> <PDBx:fract_z>0.758</PDBx:fract_z> <PDBx:B_iso>40.8</PDBx:B_iso> </PDBx:phasing_MIR_der_site> <PDBx:phasing_MIR_der_site der_id="K3IrCl6" id="2"> <PDBx:atom_type_symbol>Ir</PDBx:atom_type_symbol> <PDBx:occupancy>0.05</PDBx:occupancy> <PDBx:fract_x>0.279</PDBx:fract_x> <PDBx:fract_y>0.613</PDBx:fract_y> <PDBx:fract_z>0.752</PDBx:fract_z> <PDBx:B_iso>24.9</PDBx:B_iso> </PDBx:phasing_MIR_der_site> </PDBx:phasing_MIR_der_siteCategory> Isotropic temperature factor for this heavy-atom site in this derivative. The estimated standard deviation of attribute B_iso in category phasing_MIR_der_site. The x coordinate of this heavy-atom position in this derivative specified as orthogonal angstroms. The orthogonal Cartesian axes are related to the cell axes as specified by the description given in attribute Cartn_transform_axes in category atom_sites. The estimated standard deviation of attribute Cartn_x in category phasing_MIR_der_site. The y coordinate of this heavy-atom position in this derivative specified as orthogonal angstroms. The orthogonal Cartesian axes are related to the cell axes as specified by the description given in attribute Cartn_transform_axes in category atom_sites. The estimated standard deviation of attribute Cartn_y in category phasing_MIR_der_site. The z coordinate of this heavy-atom position in this derivative specified as orthogonal angstroms. The orthogonal Cartesian axes are related to the cell axes as specified by the description given in attribute Cartn_transform_axes in category atom_sites. The estimated standard deviation of attribute Cartn_z in category phasing_MIR_der_site. This data item is a pointer to attribute symbol in category atom_type in the ATOM_TYPE category. The scattering factors referenced via this data item should be those used in the refinement of the heavy atom data; in some cases this is the scattering factor to the single heavy atom, in others these are the scattering factors for an atomic cluster. A description of special aspects of the derivative site. binds to His 117 minor site obtained from difference Fourier same as site 2 in the K2HgI4 derivative The x coordinate of this heavy-atom position in this derivative specified as a fraction of attribute length_a in category cell. The estimated standard deviation of attribute fract_x in category phasing_MIR_der_site. The y coordinate of this heavy-atom position in this derivative specified as a fraction of attribute length_b in category cell. The estimated standard deviation of attribute fract_y in category phasing_MIR_der_site. The z coordinate of this heavy-atom position in this derivative specified as a fraction of attribute length_c in category cell. The estimated standard deviation of attribute fract_z in category phasing_MIR_der_site. The fraction of the atom type present at this heavy-atom site in a given derivative. The sum of the occupancies of all the atom types at this site may not significantly exceed 1.0 unless it is a dummy site. The relative anomalous occupancy of the atom type present at this heavy-atom site in a given derivative. This atom occupancy will probably be on an arbitrary scale. The standard uncertainty (e.s.d.) of attribute occupancy_anom in category phasing_MIR_der_site. The relative real isotropic occupancy of the atom type present at this heavy-atom site in a given derivative. This atom occupancy will probably be on an arbitrary scale. The standard uncertainty (e.s.d.) of attribute occupancy_iso in category phasing_MIR_der_site. This data item is a pointer to attribute id in category phasing_MIR_der in the PHASING_MIR_DER category. The value of attribute id in category phasing_MIR_der_site must uniquely identify each site in each derivative in the PHASING_MIR_DER_SITE list. The atom identifiers need not be unique over all sites in all derivatives; they need only be unique for each site in each derivative. Note that this item need not be a number; it can be any unique identifier. Data items in the PHASING_MIR_SHELL category record details broken down into shells of resolution, when the phasing method involves isomorphous replacement. Example 1 - based on a paper by Zanotti et al. [(1993). J. Biol. Chem. 268, 10728-10738]. with addition of an arbitrary low-resolution limit <PDBx:phasing_MIR_shellCategory> <PDBx:phasing_MIR_shell d_res_low="15.0" d_res_high="8.3"> <PDBx:reflns>80</PDBx:reflns> <PDBx:fom>0.69</PDBx:fom> </PDBx:phasing_MIR_shell> <PDBx:phasing_MIR_shell d_res_low="8.3" d_res_high="6.4"> <PDBx:reflns>184</PDBx:reflns> <PDBx:fom>0.73</PDBx:fom> </PDBx:phasing_MIR_shell> <PDBx:phasing_MIR_shell d_res_low="6.4" d_res_high="5.2"> <PDBx:reflns>288</PDBx:reflns> <PDBx:fom>0.72</PDBx:fom> </PDBx:phasing_MIR_shell> <PDBx:phasing_MIR_shell d_res_low="5.2" d_res_high="4.4"> <PDBx:reflns>406</PDBx:reflns> <PDBx:fom>0.65</PDBx:fom> </PDBx:phasing_MIR_shell> <PDBx:phasing_MIR_shell d_res_low="4.4" d_res_high="3.8"> <PDBx:reflns>554</PDBx:reflns> <PDBx:fom>0.54</PDBx:fom> </PDBx:phasing_MIR_shell> <PDBx:phasing_MIR_shell d_res_low="3.8" d_res_high="3.4"> <PDBx:reflns>730</PDBx:reflns> <PDBx:fom>0.53</PDBx:fom> </PDBx:phasing_MIR_shell> <PDBx:phasing_MIR_shell d_res_low="3.4" d_res_high="3.0"> <PDBx:reflns>939</PDBx:reflns> <PDBx:fom>0.50</PDBx:fom> </PDBx:phasing_MIR_shell> </PDBx:phasing_MIR_shellCategory> The mean value of the figure of merit m for acentric reflections in this shell. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~a~ = the probability that phase angle a is correct the integral is taken over the range alpha = 0 to 2 pi. The mean value of the figure of merit m for centric reflections in this shell. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~a~ = the probability that phase angle a is correct the integral is taken over the range alpha = 0 to 2 pi. Residual factor R~cullis~ for centric reflections in this shell. sum| |Fph~obs~ +/- Fp~obs~| - Fh~calc~ | R~cullis~ = ---------------------------------------- sum|Fph~obs~ - Fp~obs~| Fp~obs~ = the observed structure factor amplitude of the native Fph~obs~ = the observed structure factor amplitude of the derivative Fh~calc~ = the calculated structure factor amplitude from the heavy atom model sum is taken over the specified reflections Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G. & North, A. C. T. (1961). Proc. R. Soc. A265, 15-38. Residual factor R~kraut~ for general reflections in this shell. sum|Fph~obs~ - Fph~calc~| R~kraut~ = ------------------------- sum|Fph~obs~| Fph~obs~ = the observed structure factor amplitude of the derivative Fph~calc~ = the calculated structure factor amplitude of the derivative sum is taken over the specified reflections Ref: Kraut, J., Sieker, L. C., High, D. F. & Freer, S. T. (1962). Proc. Natl. Acad. Sci. USA, 48, 1417-14??. The mean value of the figure of merit m for reflections in this shell. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~alpha~ = the probability that phase angle alpha is correct int is taken over the range alpha = 0 to 2 pi. The mean lack-of-closure error loc for reflections in this shell. loc = sum|Fph~obs~ - Fph~calc~| Fph~obs~ = the observed structure factor amplitude of the derivative Fph~calc~ = the calculated structure factor amplitude of the derivative sum is taken over the specified reflections The mean of the phase values for all reflections in this shell. record R_Cullis from from acentric reflection for each shell. record R_Cullis from from centric reflection for each shell. record R_kraut from from acentric reflection for each shell. record R_Kraut from from centric reflection for each shell. record lack of closure from acentric reflection for each shell. record lack of closure from centric reflection for each shell. record phasing power from acentric reflection for each shell. record phasing power from centric reflection for each shell. The mean phasing power P for reflections in this shell. sum|Fh~calc~^2^| P = (----------------------------)^1/2^ sum|Fph~obs~ - Fph~calc~|^2^ Fph~obs~ = the observed structure factor amplitude of the derivative Fph~calc~ = the calculated structure factor amplitude of the derivative Fh~calc~ = the calculated structure factor amplitude from the heavy atom model sum is taken over the specified reflections The number of reflections in this shell. The number of acentric reflections in this shell. The number of anomalous reflections in this shell. The number of centric reflections in this shell. The lowest resolution for the interplanar spacing in the reflection data in this shell. This is the largest d value. Note that the resolution limits of shells in the items _phasing_MIR_shell.d_res_high and _phasing_MIR_shell.d_res_low are independent of the resolution limits of shells in the items _reflns_shell.d_res_high and _reflns_shell.d_res_low. The highest resolution for the interplanar spacing in the reflection data in this shell. This is the smallest d value. Note that the resolution limits of shells in the items _phasing_MIR_shell.d_res_high and _phasing_MIR_shell.d_res_low are independent of the resolution limits of shells in the items _reflns_shell.d_res_high and _reflns_shell.d_res_low. Data items in the PHASING_AVERAGING category record details about the phasing of the structure, when methods involving averaging of multiple observations of the molecule in the asymmetric unit are involved. Example 1 - example is completely hypothetical <PDBx:phasing_averagingCategory> <PDBx:phasing_averaging entry_id="EXAMHYPO"> <PDBx:method> Iterative 3-fold averaging alternating with phase extensions by 0.5 reciprocal lattice units per cycle according to the method described by X and Y (ref).</PDBx:method> <PDBx:details> The position of the 3-fold axis was redetermined every five cycles.</PDBx:details> </PDBx:phasing_averaging> </PDBx:phasing_averagingCategory> A description of special aspects of the averaging process. A description of the phase averaging phasing method applied to phase this structure. Note that this is not the computer program used, which is described in the SOFTWARE category, but rather the method itself. This data item should be used to describe significant methodological options used within the phase averaging program. This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the PHASING_ISOMORPHOUS category record details about the phasing of the structure, when a model isomorphous to the structure being phased was used to generate initial phases. Example 1 - based on PDB entry 4PHV and laboratory records for the structure corresponding to PDB entry 4PHV <PDBx:phasing_isomorphousCategory> <PDBx:phasing_isomorphous> <PDBx:parent>PDB entry 5HVP</PDBx:parent> <PDBx:details> The inhibitor and all solvent atoms were removed from the parent structure before beginning refinement. All static disorder present in the parent structure was also removed.</PDBx:details> </PDBx:phasing_isomorphous> </PDBx:phasing_isomorphousCategory> A description of special aspects of the isomorphous phasing. Residues 13-18 were eliminated from the starting model as it was anticipated that binding of the inhibitor would cause a structural rearrangement in this part of the structure. A description of the isomorphous phasing method applied to phase this structure. Note that this is not the computer program used, which is described in the SOFTWARE category, but rather the method itself. This data item should be used to describe significant methodological options used within the isomorphous phasing program. Iterative 3-fold averaging alternating with phase extension by 0.5 reciprocal lattice units per cycle according to the method described by X and Y (ref). Reference to the structure used to generate starting phases if the structure referenced in this data block was phased by virtue of being isomorphous to a known structure (e.g. a mutant that crystallizes in the same space group as the wild type protein.) This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the PHASING_SET category record details about the data sets used in a phasing experiment. A given data set may be used in a number of different ways; for instance, a single data set could be used both as an isomorphous derivative and as a component of a multi-wavelength calculation. This category establishes identifiers for each data set, and permits the archiving of a subset of experimental information for each data set (cell constants, wavelength, temperature, etc.) This and related categories of data items are provided so that derivative intensity and phase information can be stored in the same data block as the information for the refined structure. If it is deemed desirable to archive all possible experimental information for each data set (raw data sets, crystal growth conditions, etc.) those data items should be recorded in a separate data block. Example 1 - based on laboratory records for a Hg/Pt derivative of protein NS1. <PDBx:phasing_setCategory> <PDBx:phasing_set id="NS1-96"> <PDBx:cell_angle_alpha>90.0</PDBx:cell_angle_alpha> <PDBx:cell_angle_beta>90.0</PDBx:cell_angle_beta> <PDBx:cell_angle_gamma>90.0</PDBx:cell_angle_gamma> <PDBx:cell_length_a>38.63</PDBx:cell_length_a> <PDBx:cell_length_b>38.63</PDBx:cell_length_b> <PDBx:cell_length_c>82.88</PDBx:cell_length_c> <PDBx:radiation_wavelength>1.5145</PDBx:radiation_wavelength> <PDBx:detector_type>image plate</PDBx:detector_type> <PDBx:detector_specific>RXII</PDBx:detector_specific> </PDBx:phasing_set> </PDBx:phasing_setCategory> Unit-cell angle alpha in degrees of the data set. Unit-cell angle beta in degrees of the data set. Unit-cell angle gamma in degrees of the data set. Unit-cell length a corresponding to the data set. Unit-cell length b corresponding to the data set. Unit-cell length c corresponding to the data set. The particular radiation detector. In general this will be a manufacturer, description, model number or some combination of these. Siemens model x Kodak XG MAR Research model y The general class of the radiation detector. multiwire imaging plate CCD film The particular source of radiation. In general this will be a manufacturer, description, or model number (or some combination of these) for laboratory sources and an institution name and beamline name for synchrotron sources. Rigaku RU200 Philips fine focus Mo NSLS beamline X8C The mean wavelength of radiation at which this data set was measured. The temperature in kelvins at which the data set was measured. The value of attribute id in category phasing_set must uniquely identify a record in the PHASING_SET list. Note that this item need not be a number; it can be any unique identifier. KAu(CN)2 K2HgI4 Data items in the PHASING_SET_REFLN category record the values of the measured structure factors used in a phasing experiment. This list may contain information from a number of different data sets; attribute set_id in category phasing_set_refln indicates the data set to which a given record corresponds. Example 1 - based on laboratory records for a Hg/Pt derivative of protein NS1. The example is given for the (15,15,32) reflection. <PDBx:phasing_set_reflnCategory> <PDBx:phasing_set_refln set_id="NS1-96" index_h="15" index_k="15" index_l="32"> <PDBx:F_meas_au>181.79</PDBx:F_meas_au> <PDBx:F_meas_sigma_au>3.72</PDBx:F_meas_sigma_au> </PDBx:phasing_set_refln> </PDBx:phasing_set_reflnCategory> The measured value of the structure factor for this reflection in this data set, in electrons. The measured value of the structure factor for this reflection in this data set, in arbitrary units. The estimated standard deviation of attribute F_meas in category phasing_set_refln in electrons. The estimated standard deviation of attribute F_meas_au, in category phasing_set_refln in arbitrary units. Miller index h of this reflection in this data set. Miller index k of this reflection in this data set. Miller index l of this reflection in this data set. This data item is a pointer to attribute id in category phasing_set in the PHASING_SET category. Data items in the PUBL category are used when submitting a manuscript for publication. Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. <PDBx:publCategory> <PDBx:publ> <PDBx:section_title> trans-3-Benzoyl-2-(tert-butyl)-4-(iso-butyl)-1,3-oxazolidin-5-one</PDBx:section_title> <PDBx:section_abstract> The oxazolidinone ring is a shallow envelope conformation with the tert-butyl and iso-butyl groups occupying trans-positions with respect to the ring. The angles at the N atom sum to 356.2\&#37;, indicating a very small degree of pyramidalization at this atom. This is consistent with electron delocalization between the N atom and the carbonyl centre [N-C=O = 1.374(3)\&#37;A].</PDBx:section_abstract> </PDBx:publ> </PDBx:publCategory> Example 1 - based on C~31~H~48~N~4~O~4~, reported by Coleman, Patrick, Andersen & Rettig [(1996). Acta Cryst. C52, 1525-1527]. <PDBx:publCategory> <PDBx:publ> <PDBx:section_title> Hemiasterlin Methyl Ester</PDBx:section_title> <PDBx:section_title_footnote> IUPAC name: methyl 2,5-dimethyl-4-{2-[3-methyl- 2-methylamino-3-(N-methylbenzo[b]pyrrol- 3-yl)butanamido]-3,3-dimethyl-N-methyl- butanamido}-2-hexenoate.</PDBx:section_title_footnote> </PDBx:publ> </PDBx:publCategory> The name and address of the author submitting the manuscript and data block. This is the person contacted by the journal editorial staff. It is preferable to use the separate data items _publ_contact_author_name and attribute in category publ_contact_author_address. Professor George Ferguson Department of Chemistry and Biochemistry University of Guelph Ontario Canada N1G 2W1 The address of the author submitting the manuscript and data block. This is the person contacted by the journal editorial staff. Department of Chemistry and Biochemistry University of Guelph Ontario Canada N1G 2W1 Email address in a form recognisable to international networks. name@host.domain.country uur5@banjo.bitnet Facsimile telephone number of the author submitting the manuscript and data block. The recommended style includes the international dialing prefix, the area code in parentheses, followed by the local number with no spaces. The earlier convention of including the international dialing prefixes in parentheses is no longer recommended. 12(34)9477330 12()349477330 The name of the author submitting the manuscript and data block. This is the person contacted by the journal editorial staff. Professor George Ferguson Telephone number of the author submitting the manuscript and data block. The recommended style includes the international dialing prefix, the area code in parentheses, followed by the local number and any extension number prefixed by 'x', with no spaces. The earlier convention of including the international dialing prefixes in parentheses is no longer recommended. 12(34)9477330 12()349477330 12(34)9477330x5543 A letter submitted to the journal editor by the contact author. A description of the word processor package and computer used to create the word processed manuscript stored as attribute in category publ_manuscript_processed. Tex file created by FrameMaker on a Sun 3/280 The full manuscript of a paper (excluding possibly the figures and the tables) output in ASCII characters from a word processor. Information about the generation of this data item must be specified in the data item attribute in category publ_manuscript_creation. The full manuscript of a paper (excluding figures and possibly the tables) output as standard ASCII text. The category of paper submitted. For submission to Acta Crystallographica Section C, ONLY those codes indicated for use with that journal should be used. The name of the Co-editor whom the authors would like to process the submitted manuscript. The name of the journal to which the manuscript is being submitted. The abstract section of a manuscript if the manuscript is submitted in parts. As an alternative see attribute manuscript_text in category publ and attribute in category publ_manuscript_processed. The acknowledgements section of a manuscript if the manuscript is submitted in parts. As an alternative see attribute manuscript_text in category publ and attribute in category publ_manuscript_processed. The comment section of a manuscript if the manuscript is submitted in parts. As an alternative see attribute manuscript_text in category publ and attribute in category publ_manuscript_processed. The discussion section of a manuscript if the manuscript is submitted in parts. As an alternative see attribute manuscript_text in category publ and attribute in category publ_manuscript_processed. The experimental section of a manuscript if the manuscript is submitted in parts. As an alternative see attribute manuscript_text in category publ and attribute in category publ_manuscript_processed The _publ.section_exptl_prep, _publ.section_exptl_solution and attribute section_exptl_refinement in category publ items are preferred for separating the chemical preparation, structure solution and refinement aspects of the experimental description. The experimental preparation section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ_manuscript_processed. The experimental refinement section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ_manuscript_processed. The experimental solution section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ_manuscript_processed. The figure captions section of a manuscript if the manuscript is submitted in parts. As an alternative see attribute manuscript_text in category publ and attribute in category publ_manuscript_processed. The introduction section of a manuscript if the manuscript is submitted in parts. As an alternative see attribute manuscript_text in category publ and attribute in category publ_manuscript_processed. The references section of a manuscript if the manuscript is submitted in parts. As an alternative see attribute manuscript_text in category publ and attribute in category publ_manuscript_processed. The synopsis section of a manuscript if the manuscript is submitted in parts. As an alternative see attribute manuscript_text in category publ and attribute in category publ_manuscript_processed. The table legends section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ_manuscript_processed. The title of a manuscript if the manuscript is submitted in parts. As an alternative see attribute manuscript_text in category publ and attribute in category publ_manuscript_processed. The title footnote section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ_manuscript_processed. This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the PUBL_AUTHOR category record details of the authors of a manuscript submitted for publication. Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. <PDBx:publ_authorCategory> <PDBx:publ_author name="Willis, Anthony C."> <PDBx:address> Research School of Chemistry Australian National University GPO Box 4 Canberra, A.C.T. Australia 2601</PDBx:address> </PDBx:publ_author> </PDBx:publ_authorCategory> The address of a publication author. If there is more than one author this is looped with attribute name in category publ_author. Department Institute Street City and postcode COUNTRY A footnote accompanying an author's name in the list of authors of a paper. Typically indicates sabbatical address, additional affiliations or date of decease. On leave from U. Western Australia Also at Department of Biophysics The name of a publication author. If there are multiple authors they will be looped with attribute in category publ_author_address. The family name(s), followed by a comma and including any dynastic components, precedes the first names or initials. Bleary, Percival R. O'Neil, F.K. Van den Bossche, G. Yang, D.-L. Simonov, Yu.A Data items in the PUBL_BODY category permit labelling of different text sections within the body of a submitted paper. Note that these should not be used in a paper which has a standard format with sections tagged by specific data names (such as in Acta Crystallographica Section C). Typically, each journal will supply a list of the specific items it requires in its Notes for Authors. Example 1 - based on a paper by R. Restori & D. Schwarzenbach [(1996). Acta Cryst. A52, 369-378]. <PDBx:publ_bodyCategory> <PDBx:publ_body element="section" label="1"> <PDBx:title>Introduction</PDBx:title> <PDBx:format>cif</PDBx:format> <PDBx:contents> X-ray diffraction from a crystalline material provides information on the thermally and spatially averaged electron density in the crystal...</PDBx:contents> </PDBx:publ_body> <PDBx:publ_body element="section" label="2"> <PDBx:title>Theory</PDBx:title> <PDBx:format>tex</PDBx:format> <PDBx:contents> In the rigid-atom approximation, the dynamic electron density of an atom is described by the convolution product of the static atomic density and a probability density function, $\rho_{dyn}(\bf r) = \rho_{stat}(\bf r) * P(\bf r). \eqno(1) $</PDBx:contents> </PDBx:publ_body> </PDBx:publ_bodyCategory> Example 2 - based on a paper by R. J. Papoular, Y. Vekhter & P. Coppens (1996), Acta Cryst. A52, 397-407. <PDBx:publ_bodyCategory> <PDBx:publ_body element="section" label="3"> <PDBx:title> The two-channel method for retrieval of the deformation electron density</PDBx:title> </PDBx:publ_body> <PDBx:publ_body element="subsection" label="3.1"> <PDBx:title>The two-channel entropy S[\D\r(r)]</PDBx:title> <PDBx:contents> As the wide dynamic range involved in the total electron density...</PDBx:contents> </PDBx:publ_body> <PDBx:publ_body element="subsection" label="3.2"> <PDBx:title>Uniform vs informative prior model densities</PDBx:title> </PDBx:publ_body> <PDBx:publ_body element="subsubsection" label="3.2.1"> <PDBx:title>Use of uniform models</PDBx:title> <PDBx:contents> Straightforward algebra leads to expressions analogous to...</PDBx:contents> </PDBx:publ_body> </PDBx:publ_bodyCategory> A text section of a submitted paper. Code indicating the appropriate typesetting conventions for accented characters and special symbols in the text section. Title of the associated section of text. The functional role of the associated text section. Code identifying the section of text. 1 1.1 2.1.3 Data items in the PUBL_MANUSCRIPT_INCL category allow the authors of a manuscript submitted for publication to list data names that should be added to the standard request list employed by journal printing software. Example 1 - Example is completely hypothetical. <PDBx:publ_manuscript_inclCategory> <PDBx:publ_manuscript_incl> <PDBx:extra_item>_atom_site_symmetry_multiplicity</PDBx:extra_item> <PDBx:extra_info>to emphasise very special sites</PDBx:extra_info> <PDBx:extra_defn>yes</PDBx:extra_defn> </PDBx:publ_manuscript_incl> <PDBx:publ_manuscript_incl> <PDBx:extra_item>_chemical_compound_source</PDBx:extra_item> <PDBx:extra_info>rare material from unusual source</PDBx:extra_info> <PDBx:extra_defn>yes</PDBx:extra_defn> </PDBx:publ_manuscript_incl> <PDBx:publ_manuscript_incl> <PDBx:extra_item>_reflns_d_resolution_high</PDBx:extra_item> <PDBx:extra_info>the limited data is a problem here</PDBx:extra_info> <PDBx:extra_defn>yes</PDBx:extra_defn> </PDBx:publ_manuscript_incl> <PDBx:publ_manuscript_incl> <PDBx:extra_item>_crystal_magnetic_permeability</PDBx:extra_item> <PDBx:extra_info>a new data quantity needed here</PDBx:extra_info> <PDBx:extra_defn>no</PDBx:extra_defn> </PDBx:publ_manuscript_incl> </PDBx:publ_manuscript_inclCategory> Flags whether the corresponding data item marked for inclusion in a journal request list is a standard CIF definition or not (flags are 'yes' or 'no'). A short note indicating the reason why the author wishes the corresponding data item marked for inclusion in the journal request list to be published. to emphasise very special sites rare material from unusual source the limited data is a problem here a new data quantity needed here Specifies the inclusion of specific data into a manuscript which is not normally requested by the journal. The values of this item are the extra data names (which MUST be enclosed in single quotes) that will be added to the journal request list. _atom_site_symmetry_multiplicity _chemical_compound_source _reflns_d_resolution_high _crystal_magnetic_permeability This data item is a pointer to attribute id in category entry in the ENTRY category. <PDBx:rcsb_columninfoCategory> <PDBx:rcsb_columninfo tablename="summary" columnname="id"> <PDBx:description>id code</PDBx:description> <PDBx:example>id1, id2</PDBx:example> <PDBx:type>1</PDBx:type> <PDBx:table_serial_no>1</PDBx:table_serial_no> <PDBx:column_serial_no>1</PDBx:column_serial_no> <PDBx:WWW_Selection_Criteria>1</PDBx:WWW_Selection_Criteria> <PDBx:WWW_Report_Criteria>1</PDBx:WWW_Report_Criteria> </PDBx:rcsb_columninfo> </PDBx:rcsb_columninfoCategory> SQL column visibility in WWW reports queries. 0=no, 1=yes SQL column visibility in WWW selection querires. 0=no, 1=yes SQL column serial number. 1,2,3,4,... SQL column description. Table of solvent coordinates SQL column example. Table of solvent coordinates SQL table serial number. 1,2,3,4,... SQL column type. 1:integer, 2:float, 3:string-single-left, 4:string-single-right, 5:string-multi-left, 6:string-multi-right, 7:angle, 8:boolean, 9:single character, 10:author or atom name column, 11: Date SQL table name. structure_summary SQL column name. id <PDBx:rcsb_tableinfoCategory> <PDBx:rcsb_tableinfo tablename="summary"> <PDBx:description>summary data</PDBx:description> <PDBx:type>1</PDBx:type> <PDBx:table_serial_no>1</PDBx:table_serial_no> <PDBx:group_name>STRUCTURE</PDBx:group_name> <PDBx:WWW_Selection_Criteria>1</PDBx:WWW_Selection_Criteria> <PDBx:WWW_Report_Criteria>1</PDBx:WWW_Report_Criteria> </PDBx:rcsb_tableinfo> </PDBx:rcsb_tableinfoCategory> SQL table visibility in WWW reports queries. 0=no, 1=yes SQL table visibility in WWW selection querires. 0=no, 1=yes SQL column serial number. 1,2,3,4,... SQL table description. Table of solvent coordinates SQL table group name.. STRUCTURE FEATURES, SOURCE ORGANISM SQL table serial number. 1,2,3,4,... SQL table type. 0=general, 1=coordinate, 2=derived, 3=schema SQL table name. structure_summary Data items in the REFINE category record details about the structure refinement parameters. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:refineCategory> <PDBx:refine entry_id="5HVP"> <PDBx:ls_number_reflns_obs>12901</PDBx:ls_number_reflns_obs> <PDBx:ls_number_restraints>6609</PDBx:ls_number_restraints> <PDBx:ls_number_parameters>7032</PDBx:ls_number_parameters> <PDBx:ls_weighting_scheme>calc</PDBx:ls_weighting_scheme> <PDBx:ls_weighting_details> Sigdel model of Konnert-Hendrickson: Sigdel: Afsig + Bfsig*(sin(theta)/lambda-1/6) Afsig = 22.0, Bfsig = -150.0 at the beginning of refinement. Afsig = 15.5, Bfsig = -50.0 at the end of refinement.</PDBx:ls_weighting_details> </PDBx:refine> </PDBx:refineCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. <PDBx:refineCategory> <PDBx:refine> <PDBx:details>sfls:_F_calc_weight_full_matrix</PDBx:details> <PDBx:ls_structure_factor_coef>F</PDBx:ls_structure_factor_coef> <PDBx:ls_matrix_type>full</PDBx:ls_matrix_type> <PDBx:ls_weighting_scheme>calc w=1/(\s^2^(F)+0.0004F^2^)</PDBx:ls_weighting_scheme> <PDBx:ls_hydrogen_treatment>refxyz except H332B noref</PDBx:ls_hydrogen_treatment> <PDBx:ls_extinction_method>Zachariasen</PDBx:ls_extinction_method> <PDBx:ls_extinction_coef>3514(42)</PDBx:ls_extinction_coef> <PDBx:ls_extinction_expression>equ(22) p292 &quot;Crystallographic Computing&quot; (1970)</PDBx:ls_extinction_expression> <PDBx:ls_abs_structure_details> The absolute configuration was assigned to agree with the known chirality at C3 arising from its precursor l-leucine.</PDBx:ls_abs_structure_details> <PDBx:ls_abs_structure_Flack>0</PDBx:ls_abs_structure_Flack> <PDBx:ls_number_reflns_obs>1408</PDBx:ls_number_reflns_obs> <PDBx:ls_number_parameters>272</PDBx:ls_number_parameters> <PDBx:ls_number_restraints>0</PDBx:ls_number_restraints> <PDBx:ls_number_constraints>0</PDBx:ls_number_constraints> <PDBx:ls_R_factor_all>.038</PDBx:ls_R_factor_all> <PDBx:ls_R_factor_obs>.034</PDBx:ls_R_factor_obs> <PDBx:ls_wR_factor_all>.044</PDBx:ls_wR_factor_all> <PDBx:ls_wR_factor_obs>.042</PDBx:ls_wR_factor_obs> <PDBx:ls_goodness_of_fit_all>1.462</PDBx:ls_goodness_of_fit_all> <PDBx:ls_goodness_of_fit_obs>1.515</PDBx:ls_goodness_of_fit_obs> <PDBx:ls_shift_over_esd_max>.535</PDBx:ls_shift_over_esd_max> <PDBx:ls_shift_over_esd_mean>.044</PDBx:ls_shift_over_esd_mean> <PDBx:diff_density_min>-.108</PDBx:diff_density_min> <PDBx:diff_density_max>.131</PDBx:diff_density_max> </PDBx:refine> </PDBx:refineCategory> The maximum value for isotropic B value (temperature factors) found in the coordinate set. The mean value for isotropic B value (temperature factors) found in the coordinate set. The minimum value for isotropic B value (temperature factors) found in the coordinate set. The [1][1] element of the matrix that defines the overall anisotropic thermal model, if one was refined for this structure. The [1][2] element of the matrix that defines the overall anisotropic thermal model, if one was refined for this structure. The [1][3] element of the matrix that defines the overall anisotropic thermal model, if one was refined for this structure. The [2][2] element of the matrix that defines the overall anisotropic thermal model, if one was refined for this structure. The [2][3] element of the matrix that defines the overall anisotropic thermal model, if one was refined for this structure. The [3][3] element of the matrix that defines the overall anisotropic thermal model, if one was refined for this structure. The correlation coefficient between the observed and calculated structure factors for reflections included in the refinement. The correlation coefficient is scale independent and gives an idea of the quality of the refined model. sum~i~(Fo~i~ Fc~i~ - <Fo><Fc>) R~corr~ = ------------------------------------------------------------ SQRT{sum~i~(Fo~i~)^2^-<Fo>^2^} SQRT{sum~i~(Fc~i~)^2^-<Fc>^2^} Fo = observed structure factors Fc = calculated structure factors <> = denotes average value summation is over reflections included in the refinement The correlation coefficient between the observed and calculated structure factors for reflections not included in the refinement (free reflections). The correlation coefficient is scale independent and gives an idea of the quality of the refined model. sum~i~(Fo~i~ Fc~i~ - <Fo><Fc>) R~corr~ = ------------------------------------------------------------ SQRT{sum~i~(Fo~i~)^2^-<Fo>^2^} SQRT{sum~i~(Fc~i~)^2^-<Fc>^2^} Fo = observed structure factors Fc = calculated structure factors <> = denotes average value summation is over reflections not included (free reflections) in the refinement Description of special aspects of the refinement process. The maximum value of the electron density in the final difference Fourier map. The estimated standard deviation of attribute diff_density_max in category refine. The minimum value of the electron density in the final difference Fourier map. The estimated standard deviation of attribute diff_density_min in category refine. The root-mean-square-deviation of the electron density in the final difference Fourier map. This value is measured with respect to the arithmetic mean density, and is derived from summations over each grid point in the asymmetric unit of the cell. This quantity is useful for assessing the significance of the values of _refine.diff_density_min and _refine.diff_density_max, and also for defining suitable contour levels. The estimated standard deviation of attribute diff_density_rms in category refine. Residual factor R(Fsqd) for reflections that satisfy the resolution limits established by attribute ls_d_res_high in category refine and attribute ls_d_res_low in category refine and the observation limit established by attribute observed_criterion in category reflns calculated on the squares of the observed and calculated structure factor amplitudes. sum|F~obs~^2^ - F~calc~^2^| R(Fsqd) = --------------------------- sum|F~obs~^2^| F~obs~^2^ = squares of the observed structure factor amplitudes F~calc~^2^ = squares of the calculated structure factor amplitudes sum is taken over the specified reflections Residual factor R(I) for reflections that satisfy the resolution limits established by attribute ls_d_res_high in category refine and attribute ls_d_res_low in category refine and the observation limit established by attribute observed_criterion in category reflns calculated on the estimated reflection intensities. This is most often calculated in Rietveld refinements of powder data, where it is referred to as R~B~ or R~Bragg~. sum|I~obs~ - I~calc~| R(I) = --------------------- sum|I~obs~| I~obs~ = the net observed intensities I~calc~ = the net calculated intensities sum is taken over the specified reflections Residual factor R for reflections that satisfy the resolution limits established by attribute ls_d_res_high in category refine and attribute ls_d_res_low in category refine and the observation limit established by attribute observed_criterion in category reflns and that were used as the test (i.e., excluded from refinement) reflections when refinement included calculation of a "free" R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details. in category reflns sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure factor amplitudes F~calc~ = the calculated structure factor amplitudes sum is taken over the specified reflections The estimated error in attribute ls_R_factor_R_free. in category refine The method used to estimate the error is described in the item attribute ls_R_factor_R_free_error_details in category refine. Special aspects of the method used to estimated the error in attribute ls_R_factor_R_free in category refine. Residual factor R for reflections that satisfy the resolution limits established by attribute ls_d_res_high in category refine and attribute ls_d_res_low in category refine and the observation limit established by attribute observed_criterion in category reflns and that were used as the working (i.e., included in refinement) reflections when refinement included calculation of a "free" R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details. in category reflns attribute ls_R_factor_obs in category refine should not be confused with attribute ls_R_factor_R_work in category refine the former reports the results of a refinement in which all observed reflections were used, the latter a refinement in which a subset of the observed reflections were excluded from refinement for the calculation of a "free" R factor. However, it would be meaningful to quote both values if a "free" R factor were calculated for most of the refinement, but all of the observed reflections were used in the final rounds of refinement; such a protocol should be explained in attribute details. in category refine sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure factor amplitudes F~calc~ = the calculated structure factor amplitudes sum is taken over the specified reflections Residual factor R for all reflections that satisfy the resolution limits established by attribute ls_d_res_high in category refine and attribute ls_d_res_low. in category refine sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure factor amplitudes F~calc~ = the calculated structure factor amplitudes sum is taken over the specified reflections Residual factor R for reflections that satisfy the resolution limits established by attribute ls_d_res_high in category refine and attribute ls_d_res_low in category refine and the observation limit established by attribute observed_criterion. in category reflns attribute ls_R_factor_obs in category refine should not be confused with attribute ls_R_factor_R_work in category refine the former reports the results of a refinement in which all observed reflections were used, the latter a refinement in which a subset of the observed reflections were excluded from refinement for the calculation of a "free" R factor. However, it would be meaningful to quote both values if a "free" R factor were calculated for most of the refinement, but all of the observed reflections were used in the final rounds of refinement; such a protocol should be explained in attribute details. in category refine sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure factor amplitudes F~calc~ = the calculated structure factor amplitudes sum is taken over the specified reflections The measure of absolute structure (enantiomorph or polarity) as defined by Flack. The value must be between 0. and 1. with a standard uncertainty (e.s.d.). Ref: Flack, H. D. (1983). Acta Cryst. A39, 876-881. The estimated standard deviation of attribute ls_abs_structure_Flack in category refine. The measure of absolute structure (enantiomorph or polarity) as defined by Rogers. Ref: Rogers, D. (1981). Acta Cryst. A37, 734-741. The estimated standard deviation of attribute ls_abs_structure_Rogers in category refine. The nature of the absolute structure and how it was determined. For example, it may describe the Friedel pairs used. The highest resolution in angstroms for the interplanar spacing in the reflection data used in refinement. This is the smallest d value. The lowest resolution in ansgtroms for the interplanar spacing in the reflection data used in refinement. This is the largest d value. The extinction coefficient used to calculate the correction factor applied to the structure-factor data. The nature of the extinction coefficient is given in the definitions of _refine_ls_extinction_expression and attribute in category refine_ls_extinction_method For the 'Zachariasen' method it is the r* value; for the 'Becker-Coppens type 1 isotropic' method it is the 'g' value, and for 'Becker-Coppens type 2 isotropic' corrections it is the 'rho' value. Note that the magnitude of these values is usually of the order of 10000. Ref: Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30, 129-153. Zachariasen, W. H. (1967). Acta Cryst. 23, 558-564. Larson, A. C. (1967). Acta Cryst. 23, 664-665. Zachariasen coefficient r* = 0.347(5) E04 3472(52) The estimated standard deviation of attribute ls_extinction_coef in category refine. A description or reference of the extinction correction equation used to apply the data item attribute ls_extinction_coef in category refine. This information must be sufficient to reproduce the extinction correction factors applied to the structure factors. Equation (22) p292 "Crystallographic Computing" Munksgaard 1970 A description of the extinction correction method applied with the data item attribute ls_extinction_coef in category refine. This description should include information about the correction method, either 'Becker-Coppens' or 'Zachariasen' The latter is sometimes referred to as the 'Larson' method even though it employs Zachariasen's formula. The Becker-Coppens procedure is referred to as 'type 1' when correcting secondary extinction dominated by the mosaic spread; as 'type 2' when secondary extinction is dominated by particle size and includes a primary extinction component; and as 'mixed' when there is a mixture of types 1 and 2. For the Becker-Coppens method it is also necessary to set the mosaic distribution as either 'Gaussian' or 'Lorentzian'; and the nature of the extinction as 'isotropic' or 'anisotropic'. Note that if either the 'mixed' or 'anisotropic' corrections are applied the multiple coefficients cannot be contained in *_extinction_coef and must be listed in attribute details. in category refine Ref: Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30, 129-153. Zachariasen, W. H. (1967). Acta Cryst. 23, 558- 564. Larson, A. C. (1967). Acta Cryst. 23, 664-665. B-C type 2 Gaussian isotropic The least-squares goodness-of-fit parameter S for all data, after the final cycle of refinement. Ideally, account should be taken of parameters restrained in the least squares. See also the definition of attribute ls_restrained_S_all. in category refine ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ S = ( ---------------------------- ) ( N~ref~ - N~param~ ) Y~obs~ = the observed coefficients (see attribute ls_structure_factor_coef) in category refine Y~calc~ = the calculated coefficients (see attribute ls_structure_factor_coef) in category refine w = the least-squares reflection weight [1/(e.s.d. squared)] N~ref~ = the number of reflections used in the refinement N~param~ = the number of refined parameters sum is taken over the specified reflections The estimated standard deviation of attribute ls_goodness_of_fit_all in category refine. The least-squares goodness-of-fit parameter S for reflection data classified as 'observed' (see attribute observed_criterion) in category reflns after the final cycle of refinement. Ideally, account should be taken of parameters restrained in the least squares. See also the definition of attribute ls_restrained_S_obs. in category refine ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ S = ( ---------------------------- ) ( N~ref~ - N~param~ ) Y~obs~ = the observed coefficients (see attribute ls_structure_factor_coef) in category refine Y~calc~ = the calculated coefficients (see attribute ls_structure_factor_coef) in category refine w = the least-squares reflection weight [1/(e.s.d. squared)] N~ref~ = the number of reflections used in the refinement N~param~ = the number of refined parameters sum is taken over the specified reflections The estimated standard deviation of attribute ls_goodness_of_fit_obs in category refine. Treatment of hydrogen atoms in the least-squares refinement. Type of matrix used to accumulate the least-squares derivatives. The number of constrained (non-refined or dependent) parameters in the least-squares process. These may be due to symmetry or any other constraint process (e.g. rigid-body refinement). See also _atom_site.constraints and _atom_site_refinement_flags. A general description of constraints may appear in attribute details in category refine. The number of parameters refined in the least-squares process. If possible this number should include some contribution from the restrained parameters. The restrained parameters are distinct from the constrained parameters (where one or more parameters are linearly dependent on the refined value of another). Least-squares restraints often depend on geometry or energy considerations and this makes their direct contribution to this number, and to the goodness-of-fit calculation, difficult to assess. The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by attribute observed_criterion in category reflns and that were used as the test (i.e. excluded from refinement) reflections when refinement included calculation of a "free" R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details in category reflns. The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by attribute observed_criterion in category reflns and that were used as the working (i.e. included in refinement) reflections when refinement included calculation of a "free" R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details in category reflns. The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low. The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by attribute observed_criterion in category reflns. The number of restrained parameters. These are parameters which are not directly dependent on another refined parameter. Often restrained parameters involve geometry or energy dependencies. See also _atom_site.constraints and _atom_site_refinement_flags. A general description of refinement constraints may appear in attribute details in category refine. The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by attribute observed_criterion in category reflns and that were used as the test (i.e. excluded from refinement) reflections when refinement included calculation of a "free" R factor, espressed as a percentage of the number of geometrically observable reflections that satisfy the resolution limits. The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by attribute observed_criterion in category reflns expressed as a percentage of the number of geometrically observable reflections that satisfy the resolution limits. The ratio of the total number of observations of the reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low to the number of crystallographically unique reflections that satisfy those same limits. The ratio of the total number of observations of the reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by attribute observed_criterion in category reflns to the number of crystallographically unique reflections that satisfy those same limits. The least-squares goodness-of-fit parameter S' for all reflection data, after the final cycle of least squares. This parameter explicitly includes the restraints applied in the least-squares process. See also the definition of attribute ls_goodness_of_fit_all. in category refine ( sum |w |Y~obs~ - Y~calc~|^2^| )^1/2^ ( + sum~r~|w~r~ |P~calc~ - P~targ~|^2^| ) S' = ( ------------------------------------- ) ( N~ref~ + N~restr~ - N~param~ ) Y~obs~ = the observed coefficients (see attribute ls_structure_factor_coef) in category refine Y~calc~ = the observed coefficients (see attribute ls_structure_factor_coef) in category refine w = the least-squares reflection weight [1/(e.s.d. squared)] P~calc~ = the calculated restraint values P~targ~ = the target restraint values w~r~ = the restraint weight N~refr~ = the number of reflections used in the refinement (see attribute ls_number_reflns_obs) in category refine N~restr~ = the number of restraints (see attribute ls_number_restraints) in category refine N~param~ = the number of refined parameters (see attribute ls_number_parameters) in category refine sum is taken over the specified reflection data sumr is taken over the restraint data The least-squares goodness-of-fit parameter S' for reflection data classified as observed (see attribute observed_criterion) in category reflns after the final cycle of least squares. This parameter explicitly includes the restraints applied in the least-squares process. See also the definition of attribute ls_goodness_of_fit_obs. in category refine ( sum |w |Y~obs~ - Y~calc~|^2^| )^1/2^ ( + sum~r~|w~r~ |P~calc~ - P~targ~|^2^| ) S' = ( ------------------------------------- ) ( N~ref~ + N~restr~ - N~param~ ) Y~obs~ = the observed coefficients (see attribute ls_structure_factor_coef) in category refine Y~calc~ = the observed coefficients (see attribute ls_structure_factor_coef) in category refine w = the least-squares reflection weight [1/(e.s.d. squared)] P~calc~ = the calculated restraint values P~targ~ = the target restraint values w~r~ = the restraint weight N~refr~ = the number of reflections used in the refinement (see attribute ls_number_reflns_obs) in category refine N~restr~ = the number of restraints (see attribute ls_number_restraints) in category refine N~param~ = the number of refined parameters (see attribute ls_number_parameters) in category refine sum is taken over the specified reflection data sumr is taken over the restraint data The largest ratio of the final least-squares parameter shift divided by the final standard uncertainty (e.s.d.). The average ratio of the final least-squares parameter shift divided by the final standard uncertainty (e.s.d.). Structure-factor coefficient |F|, F^2^ or I, used in the least- squares refinement process. Weighted residual factor wR for reflections that satisfy the resolution limits established by attribute ls_d_res_high in category refine and attribute ls_d_res_low in category refine and the observation limit established by attribute observed_criterion in category reflns and that were used as the test (i.e., excluded from refinement) reflections when refinement included calculation of a "free" R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details. in category reflns ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by attribute ls_structure_factor_coef in category refine Y~calc~ = the calculated amplitude specified by attribute ls_structure_factor_coef in category refine w = the least squares weight sum is taken over the specified reflections Weighted residual factor wR for reflections that satisfy the resolution limits established by attribute ls_d_res_high in category refine and attribute ls_d_res_low in category refine and the observation limit established by attribute observed_criterion in category reflns and that were used as the working (i.e., included in refinement) reflections when refinement included calculation of a "free" R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details. in category reflns ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by attribute ls_structure_factor_coef in category refine Y~calc~ = the calculated amplitude specified by attribute ls_structure_factor_coef in category refine w = the least squares weight sum is taken over the specified reflections Weighted residual factor wR for all reflections that satisfy the resolution limits established by attribute ls_d_res_high in category refine and attribute ls_d_res_low. in category refine ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by attribute ls_structure_factor_coef in category refine Y~calc~ = the calculated amplitude specified by attribute ls_structure_factor_coef in category refine w = the least squares weight sum is taken over the specified reflections Weighted residual factor wR for reflections that satisfy the resolution limits established by attribute ls_d_res_high in category refine and attribute ls_d_res_low in category refine and the obervation limit established by attribute observed_criterion. in category reflns ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by attribute ls_structure_factor_coef in category refine Y~calc~ = the calculated amplitude specified by attribute ls_structure_factor_coef in category refine w = the least squares weight sum is taken over the specified reflections A description of special aspects of the weighting scheme used in least-squares refinement. Used to describe the weighting when the value of attribute ls_weighting_scheme in category refine is specified as 'calc'. Sigdel model of Konnert-Hendrickson: Sigdel = Afsig + Bfsig*(sin(theta)/lambda-1/6) Afsig = 22.0, Bfsig = 150.0 at the beginning of refinement. Afsig = 16.0, Bfsig = 60.0 at the end of refinement. The weighting scheme applied in the least-squares process. The standard code may be followed by a description of the weight (but see _refine_ls_weighting_details for a preferred approach). The maximum value for occupancy found in the coordinate set. The minimum value for occupancy found in the coordinate set. Average figure of merit of phases of reflections not included in the refinement. This value is derived from the likelihood function. FOM = I_1(X)/I_0(X) I_0, I_1 = zero- and first-order modified Bessel function of the first kind X = sigma_A |E_o| |E_c|/SIGMA E_o, E_c = normalized observed and calculated structure factors sigma_A = <cos 2 pi s delta_x> SQRT(Sigma_P/Sigma_N) estimated using maximum likelihood Sigma_P = sum_{atoms in model} f^2 Sigma_N = sum_{atoms in crystal} f^2 f = form factor of atoms delta_x = expected error SIGMA = (sigma_{E;exp})^2 + epsilon (1-{sigma_A)^2) sigma_{E;exp} = uncertainties of normalized observed structure factors epsilon = multiplicity of diffracting plane Ref: (sigma_A estimation) "Refinement of Macromolecular Structures by the Maximum-Likelihood Method", Murshudov, G. N., Vagin A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255. Average figure of merit of phases of reflections included in the refinement. This value is derived from the likelihood function. FOM = I_1(X)/I_0(X) I_0, I_1 = zero- and first-order modified Bessel function of the first kind X = sigma_A |E_o| |E_c|/SIGMA E_o, E_c = normalized observed and calculated structure factors sigma_A = <cos 2 pi s delta_x> SQRT(Sigma_P/Sigma_N) estimated using maximum likelihood Sigma_P = sum_{atoms in model} f^2 Sigma_N = sum_{atoms in crystal} f^2 f = is form factor of atoms delta_x = expected error SIGMA = (sigma_{E;exp})^2 + epsilon (1-{sigma_A)^2) sigma_{E;exp} = uncertainties of normalized observed structure factors epsilon = multiplicity of diffracting plane Ref: (sigma_A estimation) "Refinement of Macromolecular Structures by the Maximum-Likelihood Method", Murshudov, G. N., Vagin A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255. The overall standard uncertainty (e.s.d.) of the thermal parameters based on a maximum likelihood residual. The overall standard uncertainty (sigma~B~)^2 gives an idea of the uncertainty in the B values of averagely defined atoms (atoms with B values equal to the average B value). N_a (sigma~B~)^2 = 8 ---------------------------------------------- sum~i~ {(1/Sigma - (E_o)^2 (1-m^2)(SUM_AS)s^4} SUM_AS = (sigma_A)^2/Sigma^2) N_a = number of atoms Sigma = (sigma_{E;exp})^2 + epsilon (1-{sigma_A)^2) E_o = normalized structure factors sigma_{E;exp} = experimental uncertainties of normalized structure factors sigma_A = <cos 2 pi s delta_x> SQRT(Sigma_P/Sigma_N) estimated using maximum likelihood Sigma_P = sum_{atoms in model} f^2 Sigma_N = sum_{atoms in crystal} f^2 f = is form factor of atoms delta_x = expected error m = is figure of merit of phases of reflection included in summation delta_x expected error s = reciprocal space vector epsilon = multiplicity of diffracting plane summation is over all reflections included in refinement Ref: (sigma_A estimation) "Refinement of Macromolecular Structures by the Maximum-Likelihood Method", Murshudov, G. N., Vagin A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255. (SU ML estimation) "Simplified error estimation a la Cruickshank in macromolecular crystallography", Murshudov G. N. & Dodson E. J. (1997). CCP4 Newsletter, no. 33. http://www.dl.ac.uk/CCP/CCP4/newsletter33/ The overall standard uncertainty (e.s.d.) of the positional parameters based on a maximum likelihood residual. The overall standard uncertainty (sigma~X~)^2 gives an idea of the uncertainty in the position of averagely defined atoms (atoms with B values equal to average B value) 3 N_a (sigma~X~)^2 = ----------------------------------------------------- 8 pi^2 sum~i~ {(1/Sigma - (E_o)^2 (1-m^2)(SUM_AS)s^2} SUM_AS = (sigma_A)^2/Sigma^2) N_a = number of atoms Sigma = (sigma_{E;exp})^2 + epsilon (1-{sigma_A)^2) E_o = normalized structure factors sigma_{E;exp} = experimental uncertainties of normalized structure factors sigma_A = <cos 2 pi s delta_x> SQRT(Sigma_P/Sigma_N) estimated using maximum likelihood Sigma_P = sum_{atoms in model} f^2 Sigma_N = sum_{atoms in crystal} f^2 f = is form factor of atoms delta_x = expected error m = is figure of merit of phases of reflection included in summation delta_x expected error s = reciprocal space vector epsilon = multiplicity of diffracting plane summation is over all reflections included in refinement Ref: (sigma_A estimation) "Refinement of Macromolecular Structures by the Maximum-Likelihood Method", Murshudov, G. N., Vagin A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255. (SU ML estimation) "Simplified error estimation a la Cruickshank in macromolecular crystallography", Murshudov G. N. & Dodson E. J. (1997). CCP4 Newsletter, no. 33. http://www.dl.ac.uk/CCP/CCP4/newsletter33/ The overall standard uncertainty (e.s.d.) of the thermal parameters based on the crystallographic R value, expressed in a formalism known as the dispersion precision indicator (DPI). The overall standard uncertainty (sigma~B~) gives an idea of the uncertainty in the B values of averagely defined atoms (atoms with B values equal to the average B value). N_a (sigma_B)^2 = 0.65 --------- (R_value)^2 (D_min)^2 C^(-2/3) (N_o-N_p) N_a = number of atoms N_o = number of reflections included in refinement N_p = number of refined parameters R_value = conventional crystallographic R-value D_min = maximum resolution C = completeness of data Ref: Cruickshank, D. W. (1997). "Refinement of macromolecular structures". Proc. CCP4 study weekend. "Simplified error estimation a la Cruickshank in macromolecular crystallography", Murshudov G. N. & Dodson E. J. (1997). CCP4 Newsletter, no. 33. http://www.dl.ac.uk/CCP/CCP4/newsletter33/ The overall standard uncertainty (e.s.d.) of the thermal parameters based on the free R value. The overall standard uncertainty gives an idea of the uncertainty in the B values of averagely defined atoms (atoms with B values equal to the average B value). N_a (sigma_B)^2 = 0.65 ----- (R_free)^2 (D_min)^2 C^(-2/3) N_o N_a = number of atoms N_o = number of reflections included in refinement N_p = number of refined parameters R_free = conventional free crystallographic R-value calculated using reflections not included in refinement D_min = maximum resolution C = completeness of data Ref: Cruickshank, D. W. (1997). "Refinement of macromolecular structures". Proc. CCP4 study weekend. "Simplified error estimation a la Cruickshank in macromolecular crystallography", Murshudov G. N. & Dodson E. J. (1997). CCP4 Newsletter, no. 33. http://www.dl.ac.uk/CCP/CCP4/newsletter33/ Details of the manner in which the cross validation reflections were selected. Random selection Value of F at "high end" of data cutoff. 17600 Value of RMS |F| used as high data cutoff. 205.1 Value of F at "low end" of data cutoff. 0.30 Whether the structure was refined with indvidual isotropic, anisotropic or overall temperature factor. Isotropic Overall Whether the cross validataion method was used through out or only at the end. FREE R-VALUE Data cutoff (SIGMA(F)) Data cutoff (SIGMA(I)) Method(s) used to determine the structure. AB INITIO PHASING Direct Methods DM Iterative Single wavelength Anomalous Scattering ISAS Iterative Single Isomorphous Replacement ISIR Iterative Single Isomorphous Replacement with Anomalous Scattering ISIRAS Multi wavelength Anomalous Diffraction MAD Multiple Isomorphous Replacement MIR Multiple Isomorphous Replacement with Anomalous Scattering MIRAS Molecular Replacement MR Single Isomorphous Replacement SIR Single Isomorphous Replacement with Anomalous Scattering SIRAS Overall estimated standard uncertainties of positional parameters based on R value. Overall estimated standard uncertainties of positional parameters based on R value. CCP4 solvent ion proble radii CCP4 solvent shrinkage radii CCP4 solvent proble van der Waals radii Starting model for refinement. Starting model for molecular replacement should refer to a previous structure or experiment. BDL001 Special case of stereochemistry target values used in SHELXL refinement. Stereochemistry target values used in refinement. Special aspects of the solvent model used in refinement. The value of the BSOL solvent model parameter describing the average isotropic temperature factor of disordered solvent atoms. The value of the KSOL solvent model parameter describing the ratio of electron density in the bulk solvent to the electron density in the molecular solute. This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the REFINE_B_ISO category record details about the treatment of isotropic B (temperature) factors during refinement. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:refine_B_isoCategory> <PDBx:refine_B_iso class="protein"> <PDBx:treatment>isotropic</PDBx:treatment> </PDBx:refine_B_iso> <PDBx:refine_B_iso class="solvent"> <PDBx:treatment>isotropic</PDBx:treatment> </PDBx:refine_B_iso> <PDBx:refine_B_iso class="inhibitor"> <PDBx:treatment>isotropic</PDBx:treatment> </PDBx:refine_B_iso> </PDBx:refine_B_isoCategory> A description of special aspects of the isotropic B (temperature) factor refinement for the class of atoms described in attribute class in category refine_B_iso. The temperature factors of atoms in the side chain of Arg 92 were held fixed due to unstable behavior in refinement. The treatment of isotropic B (temperature) factor refinement for a class of atoms defined in attribute class in category refine_B_iso. The value of the isotropic B (temperature) factor assigned to a class of atoms defined in attribute class in category refine_B_iso. Meaningful only for atoms with fixed isotropic B (temperature) factors. A class of atoms treated similarly for isotropic B (temperature) factor refinement. all protein solvent sugar-phosphate backbone Data items in the REFINE_ANALYZE category record details about the refined structure that are often used to analyze the refinement and asses its quality. A given computer program may or may not produce values corresponding to these data names. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:refine_analyzeCategory> <PDBx:refine_analyze entry_id="5HVP"> <PDBx:Luzzati_coordinate_error_obs>0.056</PDBx:Luzzati_coordinate_error_obs> <PDBx:Luzzati_d_res_low_obs>2.51</PDBx:Luzzati_d_res_low_obs> </PDBx:refine_analyze> </PDBx:refine_analyzeCategory> The estimated coordinate error obtain from the plot of the R value versus sin(theta)/lambda for the reflections treated as a test set in refinement. Ref: Luzzati, V. (1952). Acta Cryst. 5, 134-136. The estimated coordinate error obtained from the plot of the R value versus sin(theta)/lambda for reflections classified as observed. Ref: Luzzati, V. (1952). Acta Cryst. 5, 134-136. The value of the low resolution cutoff used in constructing the Luzzati plot for reflections treated as a test set in refinement. Ref: Luzzati, V. (1952). Acta Cryst. 5, 134-136. The value of the low resolution cutoff used in constructing the Luzzati plot for reflections classified as observed. Ref: Luzzati, V. (1952). Acta Cryst. 5, 134-136. The value of sigma~a~ used in constructing the Luzzati plot for the reflections treated as a test set in refinement. The details of the estimation of sigma~a~ can be specified in attribute Luzzati_sigma_a_free_details. in category refine_analyze Ref: Luzzati, V. (1952). Acta Cryst. 5, 134-136. The details of the estimation of sigma~a~ for the reflections treated as a test set in refinement. Ref: Luzzati, V. (1952). Acta Cryst. 5, 134-136. The value of sigma~a~ used in constructing the Luzzati plot for reflections classified as observed. The details of the estimation of sigma~a~ can be specified in attribute Luzzati_sigma_a_obs_details. in category refine_analyze Ref: Luzzati, V. (1952). Acta Cryst. 5, 134-136. Special aspects of the estimation of sigma~a~ for the reflections classified as observed. Ref: Luzzati, V. (1952). Acta Cryst. 5, 134-136. The value of the high-resolution cutoff in angstroms used in calculation of the Hamilton generalized R factor (RG) stored in refine_analyze.RG_work and attribute RG_free. in category refine_analyze Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510. The value of the low-resolution cutoff in angstroms used in calculation of the Hamilton generalized R factor (RG) stored in refine_analyze.RG_work and attribute RG_free. in category refine_analyze Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510. The Hamilton generalized R factor for all reflections that satisfy the resolution limits established by attribute RG_d_res_high in category refine_analyze and attribute RG_d_res_low in category refine_analyze for the free R set of reflections that were excluded from the refinement. sum_i sum_j w_{i,j}(|Fobs|_i - G|Fcalc|_i)(|Fobs|_j - G|Fcalc|_j) Rg = Sqrt( ----------------------------------------------------------------- ) sum_i sum_j w_{i,j} |Fobs|_i |Fobs|_j where |Fobs| = the observed structure factor amplitudes |Fcalc| = the calculated structure factor amplitudes G = the scale factor which puts |Fcalc| on the same scale as |Fobs| w_{i,j} = the weight for the combination of the reflections i and j. sum_i and sum_j are taken over the specified reflections When the covariance of the amplitude of reflection i and reflection j is zero (i.e. the reflections are independent) w{i,i} can be redefined as w_i and the nested sums collapsed into one. sum_i w_i(|Fobs|_i - G|Fcalc|_i)^2 Rg = Sqrt( ----------------------------------- ) sum_i w_i |Fobs|_i^2 Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510. The observed ratio of RGfree to RGwork. The expected RG ratio is the value that should be achievable at the end of a structure refinement when only random uncorrelated errors exist in data and model provided that the observations are properly weighted. When compared with the observed RG ratio it may indicate that a structure has not reached convergence or a model has been over-refined with no corresponding improvement in the model. In an unrestrained refinement the ratio of RGfree/RGwork with only random uncorrelated errors at convergence depends only on the number of reflections and the number of parameters as: sqrt[(f + m) / (f - m) ] where f = number of included structure amplitudes and target distances, and m = number of parameters being refined. In the restrained case, RGfree is calculated from a random selection of residuals including both structure amplitudes and restraints. When restraints are included in refinement the RG ratio requires a term for the contribution to the minimized residual at convergence, Drest, due to those restraints: Drest = r - sum (w_i . (a_i)^t . (H)^-1 a_i where r is the number of geometrical, temperature factor and other restraints H is the (m,m) normal matrix given by A^t.W.A W is the (n,n) symmetric weight matrix of the included observations A is the least-squares design matrix of derivatives of order (n,m) a_i is the ith row of A Then the expected RGratio becomes sqrt [ (f + (m - r + Drest))/ (f - (m - r + Drest)) ] The expected RGfree/RGwork is not yet included in the mmCIF dictionary. Ref: "Rfree and the Rfree ratio. Part I: derivation of expected values of cross-validation residuals used in macromolecular least-squares refinement". Tickle, I. J., Laskowski, R. A. & Moss, D.S. (1998). Acta Cryst. D, in the press. The Hamilton generalized R factor for all reflections that satisfy the resolution limits established by attribute RG_d_res_high in category refine_analyze and attribute RG_d_res_low in category refine_analyze and for those reflections included in the working set when a free R set of reflections are omitted from the refinement. sum_i sum_j w_{i,j}(|Fobs|_i - G|Fcalc|_i)(|Fobs|_j - G|Fcalc|_j) Rg = Sqrt( ----------------------------------------------------------------- ) sum_i sum_j w_{i,j} |Fobs|_i |Fobs|_j where |Fobs| = the observed structure factor amplitudes |Fcalc| = the calculated structure factor amplitudes G = the scale factor which puts |Fcalc| on the same scale as |Fobs| w_{i,j} = the weight for the combination of the reflections i and j. sum_i and sum_j are taken over the specified reflections When the covariance of the amplitude of reflection i and reflection j is zero (i.e. the reflections are independent) w{i,i} can be redefined as w_i and the nested sums collapsed into one. sum_i w_i(|Fobs|_i - G|Fcalc|_i)^2 Rg = Sqrt( ----------------------------------- ) sum_i w_i |Fobs|_i^2 Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510. The number of discretely disorded residues in the refined model. The sum of the occupancies of the hydrogen atoms in the refined model. The sum of the occupancies of the non-hydrogen atoms in the refined model. record the high resolution for calculating Luzzati statistics. This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the REFINE_FUNCT_MINIMIZED category record details about the individual terms of the function minimized during refinement. Example 1 - based on RESTRAIN refinement for the CCP4 text data set toxd. <PDBx:refine_funct_minimizedCategory> <PDBx:refine_funct_minimized type="sum(W*Delta(Amplitude)^2"> <PDBx:number_terms>3009</PDBx:number_terms> <PDBx:residual>1621.3</PDBx:residual> </PDBx:refine_funct_minimized> <PDBx:refine_funct_minimized type="sum(W*Delta(Plane+Rigid)^2"> <PDBx:number_terms>85</PDBx:number_terms> <PDBx:residual>56.68</PDBx:residual> </PDBx:refine_funct_minimized> <PDBx:refine_funct_minimized type="sum(W*Delta(Distance)^2"> <PDBx:number_terms>1219</PDBx:number_terms> <PDBx:residual>163.59</PDBx:residual> </PDBx:refine_funct_minimized> <PDBx:refine_funct_minimized type="sum(W*Delta(U-tempfactors)^2"> <PDBx:number_terms>1192</PDBx:number_terms> <PDBx:residual>69.338</PDBx:residual> </PDBx:refine_funct_minimized> </PDBx:refine_funct_minimizedCategory> The number of observations in this term. For example, if the term is a residual of the X-ray intensities this item would contain the number of reflections used in the refinement. The residual for this term of the function which was minimized in refinement. The weight applied to this term of the function which was minimized in the refinement. The type of the function being minimized. Data items in the REFINE_HIST category record details about the various steps along the way in the refinement of the structure. These data items are not meant to be as thorough a description of the refinement as is provided for the final model in other categories; rather, these data items provide a mechanism for sketching out the progress of the refinement, supported by a small set of representative statistics. Example 1 - based on laboratory records for the collagen-like peptide [(POG)4 EKG (POG)5]3. <PDBx:refine_histCategory> <PDBx:refine_hist cycle_id="C134"> <PDBx:d_res_high>1.85</PDBx:d_res_high> <PDBx:d_res_low>20.0</PDBx:d_res_low> <PDBx:number_atoms_solvent>217</PDBx:number_atoms_solvent> <PDBx:number_atoms_total>808</PDBx:number_atoms_total> <PDBx:number_reflns_all>6174</PDBx:number_reflns_all> <PDBx:number_reflns_obs>4886</PDBx:number_reflns_obs> <PDBx:number_reflns_R_free>476</PDBx:number_reflns_R_free> <PDBx:number_reflns_R_work>4410</PDBx:number_reflns_R_work> <PDBx:R_factor_all>.265</PDBx:R_factor_all> <PDBx:R_factor_obs>.195</PDBx:R_factor_obs> <PDBx:R_factor_R_free>.274</PDBx:R_factor_R_free> <PDBx:R_factor_R_work>.160</PDBx:R_factor_R_work> <PDBx:details> Add majority fo solvent molecules. B factors refined by group. Continued to remove misplaced water molecules.</PDBx:details> </PDBx:refine_hist> </PDBx:refine_histCategory> Residual factor R for reflections that satisfy the resolution limits established by attribute d_res_high in category refine_hist and attribute d_res_low in category refine_hist and the observation limit established by attribute observed_criterion in category reflns and that were used as the test (i.e., excluded from refinement) reflections when refinement included calculation of a "free" R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details. in category reflns sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure factor amplitudes F~calc~ = the calculated structure factor amplitudes sum is taken over the specified reflections Residual factor R for reflections that satisfy the resolution limits established by attribute d_res_high in category refine_hist and attribute d_res_low in category refine_hist and the observation limit established by attribute observed_criterion in category reflns and that were used as the working (i.e., included in refinement) reflections when refinement included calculation of a "free" R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details. in category reflns sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure factor amplitudes F~calc~ = the calculated structure factor amplitudes sum is taken over the specified reflections Residual factor R for reflections that satisfy the resolution limits established by attribute d_res_high in category refine_hist and attribute d_res_low. in category refine_hist sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure factor amplitudes F~calc~ = the calculated structure factor amplitudes sum is taken over the specified reflections Residual factor R for reflections that satisfy the resolution limits established by attribute d_res_high in category refine_hist and attribute d_res_low in category refine_hist and the observation criterion established by attribute observed_criterion. in category reflns sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure factor amplitudes F~calc~ = the calculated structure factor amplitudes sum is taken over the specified reflections The highest resolution for the interplanar spacing in the reflection data for this cycle of refinement. The lowest resolution for the interplanar spacing in the reflection data for this cycle of refinement. Description of special aspects of this cycle of the refinement process. Residues 13-17 fit and added to model; substantial rebuilding of loop containing residues 43-48; addition of first atoms to solvent model; ten cycles of Prolsq refinement. The number of solvent atoms that were included in the model at this cycle of the refinement. The total number of atoms that were included in the model at this cycle of the refinement. The number of reflections that satisfy the resolution limits established by attribute d_res_high in category refine_hist and attribute d_res_low in category refine_hist and the observation limit established by attribute observed_criterion in category reflns and that were used as the test (i.e., excluded from refinement) reflections when refinement included calculation of a "free" R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details in category reflns. The number of reflections that satisfy the resolution limits established by attribute d_res_high in category refine_hist and attribute d_res_low in category refine_hist and the observation limit established by attribute observed_criterion in category reflns and that were used as the working (i.e., included in refinement) reflections when refinement included calculation of a "free" R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details in category reflns. The number of reflections that satisfy the resolution limits established by attribute d_res_high in category refine_hist and attribute d_res_low in category refine_hist. The number of reflections that satisfy the resolution limits established by attribute d_res_high in category refine_hist and attribute d_res_low in category refine_hist and the observation criterion established by attribute observed_criterion in category reflns. Number of carbohydrate atoms included in refinement Number of ligand atoms included in refinement Number of lipid atoms included in refinement Number of nucleic atoms included in refinement Number of protein atoms included in refinement Details of pseduo atoms used to model unexplained density The value of refine_hist.cycle_id must uniquely identify a record in the REFINE_HIST list. Note that this item need not be a number; it can be any unique identifier. Data items in the REFINE_LS_RESTR category record details about the restraints applied to various classes of parameters during least-squares refinement. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:refine_ls_restrCategory> <PDBx:refine_ls_restr type="bond_d"> <PDBx:dev_ideal_target>0.020</PDBx:dev_ideal_target> <PDBx:dev_ideal>0.018</PDBx:dev_ideal> <PDBx:number>1654</PDBx:number> <PDBx:criterion>&gt; 2\s</PDBx:criterion> <PDBx:rejects>22</PDBx:rejects> </PDBx:refine_ls_restr> <PDBx:refine_ls_restr type="angle_d"> <PDBx:dev_ideal_target>0.030</PDBx:dev_ideal_target> <PDBx:dev_ideal>0.038</PDBx:dev_ideal> <PDBx:number>2246</PDBx:number> <PDBx:criterion>&gt; 2\s</PDBx:criterion> <PDBx:rejects>139</PDBx:rejects> </PDBx:refine_ls_restr> <PDBx:refine_ls_restr type="planar_d"> <PDBx:dev_ideal_target>0.040</PDBx:dev_ideal_target> <PDBx:dev_ideal>0.043</PDBx:dev_ideal> <PDBx:number>498</PDBx:number> <PDBx:criterion>&gt; 2\s</PDBx:criterion> <PDBx:rejects>21</PDBx:rejects> </PDBx:refine_ls_restr> <PDBx:refine_ls_restr type="planar"> <PDBx:dev_ideal_target>0.020</PDBx:dev_ideal_target> <PDBx:dev_ideal>0.015</PDBx:dev_ideal> <PDBx:number>270</PDBx:number> <PDBx:criterion>&gt; 2\s</PDBx:criterion> <PDBx:rejects>1</PDBx:rejects> </PDBx:refine_ls_restr> <PDBx:refine_ls_restr type="chiral"> <PDBx:dev_ideal_target>0.150</PDBx:dev_ideal_target> <PDBx:dev_ideal>0.177</PDBx:dev_ideal> <PDBx:number>278</PDBx:number> <PDBx:criterion>&gt; 2\s</PDBx:criterion> <PDBx:rejects>2</PDBx:rejects> </PDBx:refine_ls_restr> <PDBx:refine_ls_restr type="singtor_nbd"> <PDBx:dev_ideal_target>0.500</PDBx:dev_ideal_target> <PDBx:dev_ideal>0.216</PDBx:dev_ideal> <PDBx:number>582</PDBx:number> <PDBx:criterion>&gt; 2\s</PDBx:criterion> <PDBx:rejects>0</PDBx:rejects> </PDBx:refine_ls_restr> <PDBx:refine_ls_restr type="multtor_nbd"> <PDBx:dev_ideal_target>0.500</PDBx:dev_ideal_target> <PDBx:dev_ideal>0.207</PDBx:dev_ideal> <PDBx:number>419</PDBx:number> <PDBx:criterion>&gt; 2\s</PDBx:criterion> <PDBx:rejects>0</PDBx:rejects> </PDBx:refine_ls_restr> <PDBx:refine_ls_restr type="xyhbond_nbd"> <PDBx:dev_ideal_target>0.500</PDBx:dev_ideal_target> <PDBx:dev_ideal>0.245</PDBx:dev_ideal> <PDBx:number>149</PDBx:number> <PDBx:criterion>&gt; 2\s</PDBx:criterion> <PDBx:rejects>0</PDBx:rejects> </PDBx:refine_ls_restr> <PDBx:refine_ls_restr type="planar_tor"> <PDBx:dev_ideal_target>3.0</PDBx:dev_ideal_target> <PDBx:dev_ideal>2.6</PDBx:dev_ideal> <PDBx:number>203</PDBx:number> <PDBx:criterion>&gt; 2\s</PDBx:criterion> <PDBx:rejects>9</PDBx:rejects> </PDBx:refine_ls_restr> <PDBx:refine_ls_restr type="staggered_tor"> <PDBx:dev_ideal_target>15.0</PDBx:dev_ideal_target> <PDBx:dev_ideal>17.4</PDBx:dev_ideal> <PDBx:number>298</PDBx:number> <PDBx:criterion>&gt; 2\s</PDBx:criterion> <PDBx:rejects>31</PDBx:rejects> </PDBx:refine_ls_restr> <PDBx:refine_ls_restr type="orthonormal_tor"> <PDBx:dev_ideal_target>20.0</PDBx:dev_ideal_target> <PDBx:dev_ideal>18.1</PDBx:dev_ideal> <PDBx:number>12</PDBx:number> <PDBx:criterion>&gt; 2\s</PDBx:criterion> <PDBx:rejects>1</PDBx:rejects> </PDBx:refine_ls_restr> </PDBx:refine_ls_restrCategory> A criterion used to define a parameter value that deviates significantly from its ideal value in the model obtained by restrained least-squares refinement. > 3\s For the given parameter type, the root-mean-square deviation between the ideal values used as restraints in the least-squares refinement and the values obtained by refinement. For instance, bond distances may deviate by 0.018 \%A (r.m.s.) from ideal values in current model. For the given parameter type, the target root-mean-square deviation between the ideal values used as restraints in the least-squares refinement and the values obtained by refinement. The number of parameters of this type subjected to restraint in least-squares refinement. The number of parameters of this type that deviate from ideal values by more than the amount defined in attribute criterion in category refine_ls_restr in the model obtained by restrained least-squares refinement. The weighting value applied to this type of restraint in least-squares refinement. The type of the parameter being restrained. Explicit sets of data values are provided for the programs PROTIN/PROLSQ (beginning with p_) and RESTRAIN (beginning with RESTRAIN_). As computer programs will evolve, these data values are given as examples, and not as an enumeration list. Computer programs converting a data block to a refinement table will expect the exact form of the data values given here to be used. bond distance p_bond_d bond angle expressed as a distance p_angle_d planar 1,4 distance p_planar_d x-h bond distance p_xhbond_d x-h bond angle expressed as a distance p_xhangle_d hydrogen distance p_hydrog_d special distance p_special_d planes p_planar chiral centers p_chiral single-torsion non-bonded contact p_singtor_nbd multiple-torsion non-bonded contact p_multtor_nbd possible (x...y) hydrogen-bond p_xyhbond_nbd possible (x-h...y) hydrogen-bond p_xhyhbond_nbd special torsion angle p_special_tor planar torsion angle p_planar_tor staggered torsion angle p_staggered_tor orthonormal torsion angle p_orthonormal_tor main-chain bond isotropic thermal factor p_mcbond_it main-chain angle isotropic thermal factor p_mcangle_it side-chain bond isotropic thermal factor p_scbond_it side-chain angle isotropic thermal factor p_scangle_it x-h bond isotropic thermal factor p_xhbond_it x-h angle isotropic thermal factor p_xhangle_it special isotropic thermal factor p_special_it For the program RESTRAIN, the root-mean-square deviation of the difference between the values calculated from the structures used to compile the restraints dictionary parameters and the dictionary values themselves in the distance range less than 2.12 Angstroms. RESTRAIN_Distances < 2.12 For the program RESTRAIN, the root-mean-square deviation of the difference between the values calculated from the structures used to compile the restraints dictionary parameters and the dictionary values themselves in the distance range 2.12 - 2.625 Angstroms. RESTRAIN_Distances 2.12 < D < 2.625 For the program RESTRAIN, the root-mean-square deviation of the difference between the values calculated from the structures used to compile the restraints dictionary parameters and the dictionary values themselves in the distance range greater than 2.625 Angstroms. RESTRAIN_Distances > 2.625 For the program RESTRAIN, the root-mean-square deviation of the difference between the values calculated from the structures used to compile the restraints dictionary parameters and the dictionary values themselves for peptide planes. RESTRAIN_Peptide Planes For the program RESTRAIN, the root-mean-square deviation of the difference between the values calculated from the structures used to compile the restraints dictionary parameters and the dictionary values themselves for rings and planes other than peptide planes. RESTRAIN_Ring and other planes RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.2-1.4 RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.4-1.6 RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.8-2.0 RESTRAIN_r.m.s. diffs for Uiso atoms at dist 2.0-2.2 RESTRAIN_r.m.s. diffs for Uiso atoms at dist 2.2-2.4 RESTRAIN_r.m.s. diffs for Uiso atoms at dist >2.4 Data items in the REFINE_LS_RESTR_NCS category record details about the restraints applied to atomic positions in domains related by non-crystallographic symmetry during least-squares refinement, and also about the deviation of the restrained atomic parameters at the conclusion of refinement. It is expected that these values will only be reported once for each set of restrained domains. Example 1 - based on laboratory records for the collagen-like peptide, HYP-. <PDBx:refine_ls_restr_ncsCategory> <PDBx:refine_ls_restr_ncs dom_id="d2"> <PDBx:weight_position>300.0</PDBx:weight_position> <PDBx:weight_B_iso>2.0</PDBx:weight_B_iso> <PDBx:rms_dev_position>0.09</PDBx:rms_dev_position> <PDBx:rms_dev_B_iso>0.16</PDBx:rms_dev_B_iso> <PDBx:ncs_model_details> NCS restraint for pseudo-twofold symmetry between domains d1 and d2. Position weight coefficient given in Kcal/(mol \&#37;A^2^) and isotropic B weight coefficient given in \&#37;A^2^.</PDBx:ncs_model_details> </PDBx:refine_ls_restr_ncs> </PDBx:refine_ls_restr_ncsCategory> Special aspects of the manner in which non-crystallographic restraints were applied to atomic parameters in the domain specified by attribute dom_id in category refine_ls_restr_ncs and equivalent atomic parameters in the domains against which it was restrained. record the chain ID. record the residue number . record the standard divation between one segment to another record the type of NCS restraint. (for example: tight positional) record the weight used for NCS restraint. The root-mean-square deviation in equivalent isotropic thermal factors in the domain specified by attribute dom_id in category refine_ls_restr_ncs and in the domains against which it was restrained. The root-mean-square deviation in equivalent atomic positions in the domain specified by attribute dom_id in category refine_ls_restr_ncs and in the domains against which it was restrained. The value of the weighting coefficient used in non-crystallographic restraint of isotropic thermal factors in the domain specified by attribute dom_id in category refine_ls_restr_ncs to equivalent isotropic thermal factors in the domains against which it was restrained. The value of the weighting coefficient used in non-crystallographic restraint of atomic positions in the domain specified by attribute dom_id in category refine_ls_restr_ncs to equivalent atomic positions in the domains against which it was restrained. This data item is a pointer to attribute id in category struct_ncs_dom in the STRUCT_NCS_DOM category. Data items in the REFINE_LS_RESTR_TYPE category record details about the restraints types used in the least-squares refinement. Example 1 - based on RESTRAIN refinement for the CCP4 text data set toxd. <PDBx:refine_ls_restrCategory> <PDBx:refine_ls_restr type="RESTRAIN_Distances &lt; 2.12"> <PDBx:number>509</PDBx:number> <PDBx:dev_ideal>0.005</PDBx:dev_ideal> <PDBx:dev_ideal_target>0.022</PDBx:dev_ideal_target> </PDBx:refine_ls_restr> <PDBx:refine_ls_restr type="RESTRAIN_Distances 2.12 &lt; D &lt; 2.625"> <PDBx:number>671</PDBx:number> <PDBx:dev_ideal>0.016</PDBx:dev_ideal> <PDBx:dev_ideal_target>0.037</PDBx:dev_ideal_target> </PDBx:refine_ls_restr> <PDBx:refine_ls_restr type="RESTRAIN_Distances &gt; 2.625"> <PDBx:number>39</PDBx:number> <PDBx:dev_ideal>0.034</PDBx:dev_ideal> <PDBx:dev_ideal_target>0.043</PDBx:dev_ideal_target> </PDBx:refine_ls_restr> <PDBx:refine_ls_restr type="RESTRAIN_Peptide Planes"> <PDBx:number>59</PDBx:number> <PDBx:dev_ideal>0.002</PDBx:dev_ideal> <PDBx:dev_ideal_target>0.010</PDBx:dev_ideal_target> </PDBx:refine_ls_restr> <PDBx:refine_ls_restr type="RESTRAIN_Ring and other planes"> <PDBx:number>26</PDBx:number> <PDBx:dev_ideal>0.014</PDBx:dev_ideal> <PDBx:dev_ideal_target>0.010</PDBx:dev_ideal_target> </PDBx:refine_ls_restr> <PDBx:refine_ls_restr type="RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.2-1.4"> <PDBx:number>212</PDBx:number> <PDBx:dev_ideal>0.106</PDBx:dev_ideal> </PDBx:refine_ls_restr> <PDBx:refine_ls_restr type="RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.4-1.6"> <PDBx:number>288</PDBx:number> <PDBx:dev_ideal>0.101</PDBx:dev_ideal> </PDBx:refine_ls_restr> <PDBx:refine_ls_restr type="RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.8-2.0"> <PDBx:number>6</PDBx:number> <PDBx:dev_ideal>0.077</PDBx:dev_ideal> </PDBx:refine_ls_restr> <PDBx:refine_ls_restr type="RESTRAIN_r.m.s. diffs for Uiso atoms at dist 2.0-2.2"> <PDBx:number>10</PDBx:number> <PDBx:dev_ideal>0.114</PDBx:dev_ideal> </PDBx:refine_ls_restr> <PDBx:refine_ls_restr type="RESTRAIN_r.m.s. diffs for Uiso atoms at dist 2.2-2.4"> <PDBx:number>215</PDBx:number> <PDBx:dev_ideal>0.119</PDBx:dev_ideal> </PDBx:refine_ls_restr> <PDBx:refine_ls_restr type="RESTRAIN_r.m.s. diffs for Uiso atoms at dist &gt;2.4"> <PDBx:number>461</PDBx:number> <PDBx:dev_ideal>0.106</PDBx:dev_ideal> </PDBx:refine_ls_restr> </PDBx:refine_ls_restrCategory> <PDBx:refine_ls_restr_typeCategory> <PDBx:refine_ls_restr_type type="RESTRAIN_Distances &lt; 2.12"> <PDBx:distance_cutoff_high>2.12</PDBx:distance_cutoff_high> </PDBx:refine_ls_restr_type> <PDBx:refine_ls_restr_type type="RESTRAIN_Distances 2.12 &lt; D &lt; 2.625"> <PDBx:distance_cutoff_low>2.12</PDBx:distance_cutoff_low> <PDBx:distance_cutoff_high>2.625</PDBx:distance_cutoff_high> </PDBx:refine_ls_restr_type> <PDBx:refine_ls_restr_type type="RESTRAIN_Distances &gt; 2.625"> <PDBx:distance_cutoff_low>2.625</PDBx:distance_cutoff_low> </PDBx:refine_ls_restr_type> <PDBx:refine_ls_restr_type type="RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.2-1.4"> <PDBx:distance_cutoff_low>1.2</PDBx:distance_cutoff_low> <PDBx:distance_cutoff_high>1.4</PDBx:distance_cutoff_high> </PDBx:refine_ls_restr_type> <PDBx:refine_ls_restr_type type="RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.4-1.6"> <PDBx:distance_cutoff_low>1.4</PDBx:distance_cutoff_low> <PDBx:distance_cutoff_high>1.6</PDBx:distance_cutoff_high> </PDBx:refine_ls_restr_type> <PDBx:refine_ls_restr_type type="RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.8-2.0"> <PDBx:distance_cutoff_low>1.8</PDBx:distance_cutoff_low> <PDBx:distance_cutoff_high>2.0</PDBx:distance_cutoff_high> </PDBx:refine_ls_restr_type> <PDBx:refine_ls_restr_type type="RESTRAIN_r.m.s. diffs for Uiso atoms at dist 2.0-2.2"> <PDBx:distance_cutoff_low>2.0</PDBx:distance_cutoff_low> <PDBx:distance_cutoff_high>2.2</PDBx:distance_cutoff_high> </PDBx:refine_ls_restr_type> <PDBx:refine_ls_restr_type type="RESTRAIN_r.m.s. diffs for Uiso atoms at dist 2.2-2.4"> <PDBx:distance_cutoff_low>2.2</PDBx:distance_cutoff_low> <PDBx:distance_cutoff_high>2.4</PDBx:distance_cutoff_high> </PDBx:refine_ls_restr_type> <PDBx:refine_ls_restr_type type="RESTRAIN_r.m.s. diffs for Uiso atoms at dist &gt;2.4"> <PDBx:distance_cutoff_low>2.4</PDBx:distance_cutoff_low> </PDBx:refine_ls_restr_type> </PDBx:refine_ls_restr_typeCategory> The upper limit in angstroms of the distance range applied to the current restraint type. The lower limit in angstroms of the distance range applied to the current restraint type. This data item is a pointer to attribute type in category refine_ls_restr in the REFINE_LS_RESTR category. Data items in the REFINE_LS_SHELL category record details about the results of least-squares refinement, broken out by shells of resolution. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:refine_ls_shellCategory> <PDBx:refine_ls_shell d_res_low="8.00" d_res_high="4.51"> <PDBx:number_reflns_obs>1226</PDBx:number_reflns_obs> <PDBx:R_factor_obs>0.196</PDBx:R_factor_obs> </PDBx:refine_ls_shell> <PDBx:refine_ls_shell d_res_low="4.51" d_res_high="3.48"> <PDBx:number_reflns_obs>1679</PDBx:number_reflns_obs> <PDBx:R_factor_obs>0.146</PDBx:R_factor_obs> </PDBx:refine_ls_shell> <PDBx:refine_ls_shell d_res_low="3.48" d_res_high="2.94"> <PDBx:number_reflns_obs>2014</PDBx:number_reflns_obs> <PDBx:R_factor_obs>0.160</PDBx:R_factor_obs> </PDBx:refine_ls_shell> <PDBx:refine_ls_shell d_res_low="2.94" d_res_high="2.59"> <PDBx:number_reflns_obs>2147</PDBx:number_reflns_obs> <PDBx:R_factor_obs>0.182</PDBx:R_factor_obs> </PDBx:refine_ls_shell> <PDBx:refine_ls_shell d_res_low="2.59" d_res_high="2.34"> <PDBx:number_reflns_obs>2127</PDBx:number_reflns_obs> <PDBx:R_factor_obs>0.193</PDBx:R_factor_obs> </PDBx:refine_ls_shell> <PDBx:refine_ls_shell d_res_low="2.34" d_res_high="2.15"> <PDBx:number_reflns_obs>2061</PDBx:number_reflns_obs> <PDBx:R_factor_obs>0.203</PDBx:R_factor_obs> </PDBx:refine_ls_shell> <PDBx:refine_ls_shell d_res_low="2.15" d_res_high="2.00"> <PDBx:number_reflns_obs>1647</PDBx:number_reflns_obs> <PDBx:R_factor_obs>0.188</PDBx:R_factor_obs> </PDBx:refine_ls_shell> </PDBx:refine_ls_shellCategory> Residual factor R for reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low in category refine_ls_shell and the observation limit established by attribute observed_criterion in category reflns and that were used as the test (i.e., excluded from refinement) reflections when refinement included calculation of a "free" R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details. in category reflns sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure factor amplitudes F~calc~ = the calculated structure factor amplitudes sum is taken over the specified reflections The estimated error in attribute R_factor_R_free. in category refine_ls_shell The method used to estimate the error is described in the item attribute ls_R_factor_R_free_error_details in category refine. Residual factor R for reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low in category refine_ls_shell and the observation limit established by attribute observed_criterion in category reflns and that were used as the working (i.e., included in refinement) reflections when refinement included calculation of a "free" R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details. in category reflns sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure factor amplitudes F~calc~ = the calculated structure factor amplitudes sum is taken over the specified reflections Residual factor R for reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low. in category refine_ls_shell sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure factor amplitudes F~calc~ = the calculated structure factor amplitudes sum is taken over the specified reflections Residual factor R for reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low in category refine_ls_shell and the observation criterion established by attribute observed_criterion. in category reflns sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure factor amplitudes F~calc~ = the calculated structure factor amplitudes sum is taken over the specified reflections The number of reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low in category refine_ls_shell and the observation limit established by attribute observed_criterion in category reflns and that were used as the test (i.e., excluded from refinement) reflections when refinement included calculation of a "free" R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details in category reflns. The number of reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low in category refine_ls_shell and the observation limit established by attribute observed_criterion in category reflns and that were used as the working (i.e., included in refinement) reflections when refinement included calculation of a "free" R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details in category reflns. The number of reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low in category refine_ls_shell. The number of reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low in category refine_ls_shell and the observation criterion established by attribute observed_criterion in category reflns. Total number of bins used. The number of reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low in category refine_ls_shell and the observation limit established by attribute observed_criterion in category reflns and that were used as the test (i.e., excluded from refinement) reflections when refinement included calculation of a "free" R factor, expressed as a percentage of the number of geometrically observable reflection that satisfy the reflection limits. The number of reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low in category refine_ls_shell and the observation criterion established by attribute observed_criterion in category reflns expressed as a percentage of the number of geometrically observable reflections that satisfy the resolution limits. The ratio of the total number of observations of the reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low to the number of crystallographically unique reflections that satisfy those same limits. The ratio of the total number of observations of the reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation criterion established by attribute observed_criterion in category reflns to the number of crystallographically unique reflections that satisfy those same limits. Weighted residual factor wR for reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low in category refine_ls_shell and the observation limit established by attribute observed_criterion in category reflns and that were used as the test (i.e., excluded from refinement) reflections when refinement included calculation of a "free" R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details. in category reflns ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by attribute ls_structure_factor_coef in category refine Y~calc~ = the calculated amplitude specified by attribute ls_structure_factor_coef in category refine w = the least squares weight sum is taken over the specified reflections Weighted residual factor wR for reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low in category refine_ls_shell and the observation limit established by attribute observed_criterion in category reflns and that were used as the working (i.e., included in refinement) reflections when refinement included calculation of a "free" R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details. in category reflns ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by attribute ls_structure_factor_coef in category refine Y~calc~ = the calculated amplitude specified by attribute ls_structure_factor_coef in category refine w = the least squares weight sum is taken over the specified reflections Weighted residual factor wR for reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low. in category refine_ls_shell ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by attribute ls_structure_factor_coef in category refine Y~calc~ = the calculated amplitude specified by attribute ls_structure_factor_coef in category refine w = the least squares weight sum is taken over the specified reflections Weighted residual factor wR for reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low in category refine_ls_shell and the observation criterion established by attribute observed_criterion. in category reflns ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by attribute ls_structure_factor_coef in category refine Y~calc~ = the calculated amplitude specified by attribute ls_structure_factor_coef in category refine w = the least squares weight sum is taken over the specified reflections The lowest resolution for the interplanar spacing in the reflection data in this shell. This is the smallest d value. The highest resolution for the interplanar spacing in the reflection data in this shell. This is the largest d value. Data items in the REFINE_OCCUPANCY category record details about the treatment of atomic occupancies during refinement. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:refine_occupancyCategory> <PDBx:refine_occupancy class="protein"> <PDBx:treatment>fix</PDBx:treatment> <PDBx:value>1.00</PDBx:value> </PDBx:refine_occupancy> <PDBx:refine_occupancy class="solvent"> <PDBx:treatment>fix</PDBx:treatment> <PDBx:value>1.00</PDBx:value> </PDBx:refine_occupancy> <PDBx:refine_occupancy class="inhibitor orientation 1"> <PDBx:treatment>fix</PDBx:treatment> <PDBx:value>0.65</PDBx:value> </PDBx:refine_occupancy> <PDBx:refine_occupancy class="inhibitor orientation 2"> <PDBx:treatment>fix</PDBx:treatment> <PDBx:value>0.35</PDBx:value> <PDBx:details> The inhibitor binds to the enzyme in two alternative conformations. The occupancy of each conformation was adjusted so as to result in approximately equal mean thermal factors for the atoms in each conformation.</PDBx:details> </PDBx:refine_occupancy> </PDBx:refine_occupancyCategory> A description of special aspects of the occupancy refinement for a class of atoms described in attribute class in category refine_occupancy. The inhibitor binds to the enzyme in two alternative conformations. The occupancy of each conformation was adjusted so as to result in approximately equal mean thermal factors for the atoms in each conformation. The treatment of occupancy refinement for a class of atoms described in attribute class in category refine_occupancy. The value of occupancy assigned to a class of atoms defined in attribute class in category refine_occupancy. Meaningful only for atoms with fixed occupancy. 1.0 0.41 The class of atoms treated similarly for occupancy refinement. all protein solvent sugar-phosphate backbone Data items in the REFLN category record details about the reflection data used to determine the ATOM_SITE data items. The REFLN data items refer to individual reflections and must be included in looped lists. The REFLNS data items specify the parameters that apply to all reflections. The REFLNS data items are not looped. Example 1 - based on data set fetod of Todres, Yanovsky, Ermekov & Struchkov [(1993). Acta Cryst. C49, 1352-1354]. <PDBx:reflnCategory> <PDBx:refln index_h="2" index_k="0" index_l="0"> <PDBx:F_squared_calc>85.57</PDBx:F_squared_calc> <PDBx:F_squared_meas>58.90</PDBx:F_squared_meas> <PDBx:F_squared_sigma>1.45</PDBx:F_squared_sigma> <PDBx:status>o</PDBx:status> </PDBx:refln> <PDBx:refln index_h="3" index_k="0" index_l="0"> <PDBx:F_squared_calc>15718.18</PDBx:F_squared_calc> <PDBx:F_squared_meas>15631.06</PDBx:F_squared_meas> <PDBx:F_squared_sigma>30.40</PDBx:F_squared_sigma> <PDBx:status>o</PDBx:status> </PDBx:refln> <PDBx:refln index_h="4" index_k="0" index_l="0"> <PDBx:F_squared_calc>55613.11</PDBx:F_squared_calc> <PDBx:F_squared_meas>49840.09</PDBx:F_squared_meas> <PDBx:F_squared_sigma>61.86</PDBx:F_squared_sigma> <PDBx:status>o</PDBx:status> </PDBx:refln> <PDBx:refln index_h="5" index_k="0" index_l="0"> <PDBx:F_squared_calc>246.85</PDBx:F_squared_calc> <PDBx:F_squared_meas>241.86</PDBx:F_squared_meas> <PDBx:F_squared_sigma>10.02</PDBx:F_squared_sigma> <PDBx:status>o</PDBx:status> </PDBx:refln> <PDBx:refln index_h="6" index_k="0" index_l="0"> <PDBx:F_squared_calc>82.16</PDBx:F_squared_calc> <PDBx:F_squared_meas>69.97</PDBx:F_squared_meas> <PDBx:F_squared_sigma>1.93</PDBx:F_squared_sigma> <PDBx:status>o</PDBx:status> </PDBx:refln> <PDBx:refln index_h="7" index_k="0" index_l="0"> <PDBx:F_squared_calc>1133.62</PDBx:F_squared_calc> <PDBx:F_squared_meas>947.79</PDBx:F_squared_meas> <PDBx:F_squared_sigma>11.78</PDBx:F_squared_sigma> <PDBx:status>o</PDBx:status> </PDBx:refln> <PDBx:refln index_h="8" index_k="0" index_l="0"> <PDBx:F_squared_calc>2558.04</PDBx:F_squared_calc> <PDBx:F_squared_meas>2453.33</PDBx:F_squared_meas> <PDBx:F_squared_sigma>20.44</PDBx:F_squared_sigma> <PDBx:status>o</PDBx:status> </PDBx:refln> <PDBx:refln index_h="9" index_k="0" index_l="0"> <PDBx:F_squared_calc>283.88</PDBx:F_squared_calc> <PDBx:F_squared_meas>393.66</PDBx:F_squared_meas> <PDBx:F_squared_sigma>7.79</PDBx:F_squared_sigma> <PDBx:status>o</PDBx:status> </PDBx:refln> <PDBx:refln index_h="10" index_k="0" index_l="0"> <PDBx:F_squared_calc>283.70</PDBx:F_squared_calc> <PDBx:F_squared_meas>171.98</PDBx:F_squared_meas> <PDBx:F_squared_sigma>4.26</PDBx:F_squared_sigma> <PDBx:status>o</PDBx:status> </PDBx:refln> </PDBx:reflnCategory> The calculated value of structure-factor component A, in electrons. A = |F|cos(phase) The calculated value of structure-factor component A, in arbitrary units. A = |F|cos(phase) The measured value of structure-factor component A, in electrons. A = |F|cos(phase) The measured value of structure-factor component A, in arbitrary units. A = |F|cos(phase) The calculated value of structure-factor component B, in electrons. B = |F|sin(phase) The calculated value of structure-factor component B, in arbitrary units. B = |F|sin(phase) The measured value of structure-factor component B, in electrons. B = |F|sin(phase) The measured value of structure-factor component B, in arbitrary units. B = |F|sin(phase) The calculated value of the structure factor in electrons. The calculated value of the structure factor in arbitrary units. The measured value of the structure factor in electrons. The measured value of the structure factor in arbitrary units. The standard uncertainty (e.s.d.) of attribute F_meas in category refln in electrons. The standard uncertainty (e.s.d.) of attribute F_meas_au in category refln in arbitrary units. The calculated value of the squared structure factor, in electrons squared. The measured value of the squared structure factor, in electrons squared. The standard uncertainty (derived from measurement) of the squared structure factor, in electrons squared. This data item is a pointer to attribute id in category exptl_crystal in the EXPTL_CRYSTAL category. The figure of merit m for this reflection. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~a~ = the probability that phase angle a is correct int is taken over the range alpha = 0 to 2 pi. The calculated value of the intensity, in the measured units. The measured value of the intensity, in the measured units. The standard uncertainty (derived from measurement) of the intensity, in the measured units. Mean path length in millimetres through the crystal for this reflection. The calculated value of the structure factor in arbitrary units reflecting only the contribution of the solvent model. The calculated value of the structure factor in arbitrary units including the contribution of the solvent model. The calculated structure-factor phase in degrees reflecting only the contribution of the solvent model. The calculated structure-factor phase in degrees including the contribution of the solvent model. The calculated structure-factor phase in degrees. The measured structure-factor phase in degrees. Status of reflection in the structure refinement process. This data item is a pointer to attribute group_code in category reflns_scale in the REFLNS_SCALE_GROUP category. The (sin theta)/lambda value in reciprocal angstroms for this reflection. Classification of a reflection so as to indicate its status with respect to inclusion in refinement and calculation of R factors. The symmetry reinforcement factor corresponding to the number of times the reflection indices are generated identically from the space-group symmetry operations. The number of symmetry-equivalent reflections. The equivalent reflections have the same structure-factor magnitudes because of the space-group symmetry and the Friedel relationship. The mean wavelength in angstroms of radiation used to measure this reflection. This is an important parameter for data collected using energy-dispersive detectors or the Laue method. This data item is a pointer to attribute wavelength_id in category diffrn_radiation in the DIFFRN_RADIATION category. Miller index h of the reflection. The values of the Miller indices in the REFLN category must correspond to the cell defined by cell lengths and cell angles in the CELL category. Miller index k of the reflection. The values of the Miller indices in the REFLN category must correspond to the cell defined by cell lengths and cell angles in the CELL category. Miller index l of the reflection. The values of the Miller indices in the REFLN category must correspond to the cell defined by cell lengths and cell angles in the CELL category. Data items in the REFLN_SYS_ABS category record details about the reflection data that should be systematically absent, given the designated space group. Example 1 - completely arbitrary <PDBx:refln_sys_absCategory> <PDBx:refln_sys_abs index_h="0" index_k="3" index_l="0"> <PDBx:I>28.32</PDBx:I> <PDBx:sigmaI>22.95</PDBx:sigmaI> <PDBx:I_over_sigmaI>1.23</PDBx:I_over_sigmaI> </PDBx:refln_sys_abs> <PDBx:refln_sys_abs index_h="0" index_k="5" index_l="0"> <PDBx:I>14.11</PDBx:I> <PDBx:sigmaI>16.38</PDBx:sigmaI> <PDBx:I_over_sigmaI>0.86</PDBx:I_over_sigmaI> </PDBx:refln_sys_abs> <PDBx:refln_sys_abs index_h="0" index_k="7" index_l="0"> <PDBx:I>114.81</PDBx:I> <PDBx:sigmaI>20.22</PDBx:sigmaI> <PDBx:I_over_sigmaI>5.67</PDBx:I_over_sigmaI> </PDBx:refln_sys_abs> <PDBx:refln_sys_abs index_h="0" index_k="9" index_l="0"> <PDBx:I>32.99</PDBx:I> <PDBx:sigmaI>24.51</PDBx:sigmaI> <PDBx:I_over_sigmaI>1.35</PDBx:I_over_sigmaI> </PDBx:refln_sys_abs> </PDBx:refln_sys_absCategory> The measured value of the intensity in arbitrary units. The ratio of _refln_sys_abs.I to _refln_sys_abs.sigmaI. Used to evaluate whether a reflection that should be systematically absent according to the designated space group is in fact absent. The standard uncertainty (e.s.d.) of attribute I in category refln_sys_abs in arbitrary units. Miller index h of the reflection. The values of the Miller indices in the REFLN_SYS_ABS category must correspond to the cell defined by cell lengths and cell angles in the CELL category. Miller index k of the reflection. The values of the Miller indices in the REFLN_SYS_ABS category must correspond to the cell defined by cell lengths and cell angles in the CELL category. Miller index l of the reflection. The values of the Miller indices in the REFLN_SYS_ABS category must correspond to the cell defined by cell lengths and cell angles in the CELL category. Data items in the REFLNS category record details about the reflection data used to determine the ATOM_SITE data items. The REFLN data items refer to individual reflections and must be included in looped lists. The REFLNS data items specify the parameters that apply to all reflections. The REFLNS data items are not looped. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:reflnsCategory> <PDBx:reflns entry_id="5HVP"> <PDBx:data_reduction_method> Xengen program scalei. Anomalous pairs were merged. Scaling proceeded in several passes, beginning with 1-parameter fit and ending with 3-parameter fit.</PDBx:data_reduction_method> <PDBx:data_reduction_details> Merging and scaling based on only those reflections with I &gt; \s(I).</PDBx:data_reduction_details> <PDBx:d_resolution_high>2.00</PDBx:d_resolution_high> <PDBx:d_resolution_low>8.00</PDBx:d_resolution_low> <PDBx:limit_h_max>22</PDBx:limit_h_max> <PDBx:limit_h_min>0</PDBx:limit_h_min> <PDBx:limit_k_max>46</PDBx:limit_k_max> <PDBx:limit_k_min>0</PDBx:limit_k_min> <PDBx:limit_l_max>57</PDBx:limit_l_max> <PDBx:limit_l_min>0</PDBx:limit_l_min> <PDBx:number_obs>7228</PDBx:number_obs> <PDBx:observed_criterion>&gt; 1 \s(I)</PDBx:observed_criterion> <PDBx:details>none</PDBx:details> </PDBx:reflns> </PDBx:reflnsCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. <PDBx:reflnsCategory> <PDBx:reflns> <PDBx:limit_h_min>0</PDBx:limit_h_min> <PDBx:limit_h_max>6</PDBx:limit_h_max> <PDBx:limit_k_min>0</PDBx:limit_k_min> <PDBx:limit_k_max>17</PDBx:limit_k_max> <PDBx:limit_l_min>0</PDBx:limit_l_min> <PDBx:limit_l_max>22</PDBx:limit_l_max> <PDBx:number_all>1592</PDBx:number_all> <PDBx:number_obs>1408</PDBx:number_obs> <PDBx:observed_criterion>F_&gt;_6.0_\s(F)</PDBx:observed_criterion> <PDBx:d_resolution_high>0.8733</PDBx:d_resolution_high> <PDBx:d_resolution_low>11.9202</PDBx:d_resolution_low> </PDBx:reflns> </PDBx:reflnsCategory> The value of the overall isotropic temperature factor estimated from the slope of the Wilson plot. A description of the method by which a subset of reflections was selected for exclusion from refinement so as to be used in the calculation of a "free" R factor. The data set was sorted with l varying most rapidly and h varying least rapidly. Every 10th reflection is this sorted list was excluded from refinement and included in the calculation of a "free" R factor. Residual factor Rmerge for all reflections that satisfy the resolution limits established by attribute d_resolution_high in category reflns and attribute d_resolution_low. in category reflns sum~i~(sum~j~|F~j~ - <F>|) Rmerge(F) = -------------------------- sum~i~(sum~j~<F>) F~j~ = the amplitude of the jth observation of reflection i <F> = the mean of the amplitudes of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection Residual factor Rmerge for reflections that satisfy the resolution limits established by attribute d_resolution_high in category reflns and attribute d_resolution_low in category reflns and the observation limit established by attribute observed_criterion. in category reflns sum~i~(sum~j~|F~j~ - <F>|) Rmerge(F) = -------------------------- sum~i~(sum~j~<F>) F~j~ = the amplitude of the jth observation of reflection i <F> = the mean of the amplitudes of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection The highest resolution for the interplanar spacings in the reflection data. This is the smallest d value. The lowest resolution for the interplanar spacings in the reflection data. This is the largest d value. A description of special aspects of the data reduction procedures. Merging and scaling based on only those reflections with I > sig(I). The method used in reducing the data. Note that this is not the computer program used, which is described in the SOFTWARE category, but that the method itself. This data item should be used to describe significant methodological options used within the data reduction programs. Profile fitting by method of Kabsch (1987). Scaling used spherical harmonic coefficients. A description of reflection data not covered by the other data names. It should include details of the Friedel pairs. Maximum value of Miller index h for the reflection data. This need not have the same value as attribute limit_h_max in category diffrn_reflns. Minimum value of Miller index h for the reflection data. This need not have the same value as attribute limit_h_min in category diffrn_reflns. Maximum value of Miller index k for the reflection data. This need not have the same value as attribute limit_k_max in category diffrn_reflns. Minimum value of Miller index k for the reflection data. This need not have the same value as attribute limit_k_min in category diffrn_reflns. Maximum value of Miller index l for the reflection data. This need not have the same value as attribute limit_l_max in category diffrn_reflns. Minimum value of Miller index l for the reflection data. This need not have the same value as attribute limit_l_min in category diffrn_reflns. The total number of reflections in the REFLN list (not the DIFFRN_REFLN list). This number may contain Friedel equivalent reflections according to the nature of the structure and the procedures used. The item attribute details in category reflns describes the reflection data. The number of reflections in the REFLN list (not the DIFFRN_REFLN list) classified as observed (see attribute observed_criterion). in category reflns This number may contain Friedel equivalent reflections according to the nature of the structure and the procedures used. The criterion used to classify a reflection as 'observed'. This criterion is usually expressed in terms of a sigma(I) or sigma(F) threshold. >2sigma(I) The criterion used to classify a reflection as 'observed', expressed as a upper limit in the value of F. The criterion used to classify a reflection as 'observed', expressed as a lower limit in the value of F. The criterion used to classify a reflection as 'observed', expressed as a upper limit in the value of I. The criterion used to classify a reflection as 'observed', expressed as a lower limit in the value of I. The criterion used to classify a reflection as 'observed', expressed as a multiple of the value of sigma(F). The criterion used to classify a reflection as 'observed', expressed as a multiple of the value of sigma(I). R Sym value in percent. 2.0 Overall Chi-squared statistic. The highest optical resolution for this reflection data set as determined by computational method attribute pdbx_d_res_opt_method in category reflns. 1.2 The lowest optical resolution for this reflection data set as determined by computational method attribute pdbx_d_res_opt_method in category reflns. 20.5 The computational method used to determine the optical resolution limits attribute pdbx_d_res_high_opt in category reflns and attribute pdbx_d_res_low_opt in category reflns. SFCHECK Overall <I/sigma(I)> Overall redundancy. Number of reflections rejected in scaling operations. The percentage of geometrically possible reflections represented by reflections that satisfy the resolution limits established by _reflns.d_resolution_high and _reflns.d_resolution_low and the observation limit established by attribute observed_criterion in category reflns. This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the REFLNS_SCALE category record details about the structure factor scales. They are referenced from within the REFLN list through attribute scale_group_code in category refln. Example 1 - based on laboratory records for the collagen-like peptide [(POG)4 EKG (POG)5]3. <PDBx:reflns_scaleCategory> <PDBx:reflns_scale group_code="SG1"> <PDBx:meas_F>4.0</PDBx:meas_F> </PDBx:reflns_scale> </PDBx:reflns_scaleCategory> A scale associated with attribute group_code in category reflns_scale. These codes may not correspond to those in the DIFFRN_SCALE list. A scale associated with attribute group_code in category reflns_scale. These codes may not correspond to those in the DIFFRN_SCALE list. A scale associated with attribute group_code in category reflns_scale. These codes may not correspond to those in the DIFFRN_SCALE list. The code identifying a scale attribute meas_F in category reflns_scale _reflns_scale.meas_F_squared or _reflns_scale.meas_intensity. These are linked to the REFLN list by the attribute scale_group_code in category refln. 1 2 c1 c2 Data items in the REFLNS_SHELL category record details about the reflection data used to determine the ATOM_SITE data items, as broken down by shells of resolution. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:reflns_shellCategory> <PDBx:reflns_shell d_res_high="31.38" d_res_low="3.82"> <PDBx:meanI_over_sigI_obs>69.8</PDBx:meanI_over_sigI_obs> <PDBx:number_measured_obs>9024</PDBx:number_measured_obs> <PDBx:number_unique_obs>2540</PDBx:number_unique_obs> <PDBx:percent_possible_obs>96.8</PDBx:percent_possible_obs> <PDBx:Rmerge_F_obs>1.98</PDBx:Rmerge_F_obs> </PDBx:reflns_shell> <PDBx:reflns_shell d_res_high="3.82" d_res_low="3.03"> <PDBx:meanI_over_sigI_obs>26.1</PDBx:meanI_over_sigI_obs> <PDBx:number_measured_obs>7413</PDBx:number_measured_obs> <PDBx:number_unique_obs>2364</PDBx:number_unique_obs> <PDBx:percent_possible_obs>95.1</PDBx:percent_possible_obs> <PDBx:Rmerge_F_obs>3.85</PDBx:Rmerge_F_obs> </PDBx:reflns_shell> <PDBx:reflns_shell d_res_high="3.03" d_res_low="2.65"> <PDBx:meanI_over_sigI_obs>10.5</PDBx:meanI_over_sigI_obs> <PDBx:number_measured_obs>5640</PDBx:number_measured_obs> <PDBx:number_unique_obs>2123</PDBx:number_unique_obs> <PDBx:percent_possible_obs>86.2</PDBx:percent_possible_obs> <PDBx:Rmerge_F_obs>6.37</PDBx:Rmerge_F_obs> </PDBx:reflns_shell> <PDBx:reflns_shell d_res_high="2.65" d_res_low="2.41"> <PDBx:meanI_over_sigI_obs>6.4</PDBx:meanI_over_sigI_obs> <PDBx:number_measured_obs>4322</PDBx:number_measured_obs> <PDBx:number_unique_obs>1882</PDBx:number_unique_obs> <PDBx:percent_possible_obs>76.8</PDBx:percent_possible_obs> <PDBx:Rmerge_F_obs>8.01</PDBx:Rmerge_F_obs> </PDBx:reflns_shell> <PDBx:reflns_shell d_res_high="2.41" d_res_low="2.23"> <PDBx:meanI_over_sigI_obs>4.3</PDBx:meanI_over_sigI_obs> <PDBx:number_measured_obs>3247</PDBx:number_measured_obs> <PDBx:number_unique_obs>1714</PDBx:number_unique_obs> <PDBx:percent_possible_obs>70.4</PDBx:percent_possible_obs> <PDBx:Rmerge_F_obs>9.86</PDBx:Rmerge_F_obs> </PDBx:reflns_shell> <PDBx:reflns_shell d_res_high="2.23" d_res_low="2.10"> <PDBx:meanI_over_sigI_obs>3.1</PDBx:meanI_over_sigI_obs> <PDBx:number_measured_obs>1140</PDBx:number_measured_obs> <PDBx:number_unique_obs>812</PDBx:number_unique_obs> <PDBx:percent_possible_obs>33.3</PDBx:percent_possible_obs> <PDBx:Rmerge_F_obs>13.99</PDBx:Rmerge_F_obs> </PDBx:reflns_shell> </PDBx:reflns_shellCategory> Residual factor Rmerge for all reflections that satisfy the resolution limits established by attribute d_res_high in category reflns_shell and attribute d_res_low. in category reflns_shell sum~i~(sum~j~|F~j~ - <F>|) Rmerge(F) = -------------------------- sum~i~(sum~j~<F>) F~j~ = the amplitude of the jth observation of reflection i <F> = the mean of the amplitudes of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection Residual factor Rmerge for reflections that satisfy the resolution limits established by attribute d_res_high in category reflns_shell and attribute d_res_low in category reflns_shell and the observation criterion established by attribute observed_criterion. in category reflns sum~i~(sum~j~|F~j~ - <F>|) Rmerge(F) = -------------------------- sum~i~(sum~j~<F>) F~j~ = the amplitude of the jth observation of reflection i <F> = the mean of the amplitudes of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection The value of Rmerge(I) for all reflections in a given shell. sum~i~(sum~j~|I~j~ - <I>|) Rmerge(I) = -------------------------- sum~i~(sum~j~<I>) I~j~ = the intensity of the jth observation of reflection i <I> = the mean of the intensities of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection The value of Rmerge(I) for reflections classified as 'observed' (see attribute observed_criterion) in category reflns in a given shell. sum~i~(sum~j~|I~j~ - <I>|) Rmerge(I) = -------------------------- sum~i~(sum~j~<I>) I~j~ = the intensity of the jth observation of reflection i <I> = the mean of the intensities of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection The ratio of the mean of the intensities of all reflections in this shell to the mean of the standard uncertainties of the intensities of all reflections in the resolution shell. The ratio of the mean of the intensities of the reflections classified as 'observed' (see attribute observed_criterion) in category reflns in this shell to the mean of the standard uncertainties of the intensities of the 'observed' reflections in the resolution shell. The total number of reflections measured for this resolution shell. The number of reflections classified as 'observed' (see attribute observed_criterion) in category reflns measured for this resolution shell. The number of unique reflections it is possible to measure in this reflection shell. The total number of measured reflections which are symmetrically unique after merging for this resolution shell. The total number of measured reflections classified as 'observed' (see attribute observed_criterion) in category reflns which are symmetrically unique after merging for this resolution shell. R sym value in percent. Chi-squared statistic for this resolution shell. Redundancy for the current shell. The percentage of geometrically possible reflections represented by all reflections measured for this resolution shell. The percentage of geometrically possible reflections represented by reflections classified as 'observed' (see attribute observed_criterion) in category reflns measured for this resolution shell. The highest resolution in angstroms for the interplanar spacing in the reflections in this shell. This is the smallest d value. The lowest resolution in angstroms for the interplanar spacing in the reflections in this shell. This is the largest d value. Data items in the SOFTWARE category record details about the software used in the structure analysis, which implied any software used in the generation of any data items associated with the structure determination and structure representation. These data items provide an alternative, and more thorough, method for referencing computer programs than do data items in the COMPUTING category. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:softwareCategory> <PDBx:software name="Prolsq" version="unknown"> <PDBx:type>program</PDBx:type> <PDBx:contact_author>Wayne A. Hendrickson</PDBx:contact_author> <PDBx:location>ftp://rosebud.sdsc.edu/pub/sdsc/xtal/CCP4/ccp4/</PDBx:location> <PDBx:classification>refinement</PDBx:classification> <PDBx:citation_id>ref5</PDBx:citation_id> <PDBx:language>Fortran</PDBx:language> <PDBx:compiler_name>Convex Fortran</PDBx:compiler_name> <PDBx:compiler_version>v8.0</PDBx:compiler_version> <PDBx:hardware>Convex C220</PDBx:hardware> <PDBx:os>ConvexOS</PDBx:os> <PDBx:os_version>v10.1</PDBx:os_version> <PDBx:dependencies>Requires that Protin be run first</PDBx:dependencies> <PDBx:mods>optimized</PDBx:mods> <PDBx:description>restrained least-squares refinement</PDBx:description> </PDBx:software> </PDBx:softwareCategory> This data item is a pointer to attribute id in category citation in the CITATION category. The classification of the program according to its major function. data collection data reduction phasing model building refinement validation other The compiler used to compile the software. Convex Fortran gcc DEC C The version of the compiler used to compile the software. 3.1 2.1 alpha The recognized contact author of the software. This could be the original author, modifier of the code, or maintainer, but should be the individual most commonly associated with the code. T. Alwyn Jones Axel Brunger The email address of the attribute contact_author in category software. bourne@sdsc.edu The date the software was released. 1991-10-01 1990-04-30 Any prerequisite software required to run attribute name in category software. PDBlib class library Description of the software. Uses method of restrained least squares The hardware upon which the software was run. Sun Sparc 10 model 41 Dec Alpha 3000 model 500S Silicon Graphics Elan Compaq PC 486/66 The major computing language in which the software is coded. An Internet address in the form of a URL describing where details of the software can be found. http://rosebud.sdsc.edu/projects/pb/IUCr/software.html ftp://ftp.sdsc.edu/pub/sdsc/biology/ Any noteworthy modifications to the base software, if applicable. Added support for space group F432 The name of the operating system under which the software runs. Ultrix OpenVMS DOS Windows 95 Windows NT Irix HPUX DEC Unix The version of the operating system under which the software runs. 3.1 4.2.1 The classification of the software according to the most common types. The name of the software. Merlot O Xengen X-plor The version of the software. v1.0 beta 3.1-2 unknown Data items in the STRUCT category record details about the description of the crystallographic structure. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:structCategory> <PDBx:struct entry_id="5HVP"> <PDBx:title> HIV-1 protease complex with acetyl-pepstatin</PDBx:title> </PDBx:struct> </PDBx:structCategory> An automatically generated descriptor for an NDB structure or the unstructured content of the PDB COMPND record. 5'-D(*CP*GP*CP*(HYD)AP*AP*AP*TP*TP*TP*GP*CP*G)-3' Text description of the methodology which produced this model structure. This model was produced from a 10 nanosecond Amber/MD simulation starting from PDB structure ID 1ABC. A title for the data block. The author should attempt to convey the essence of the structure archived in the CIF in the title, and to distinguish this structural result from others. 5'-D(*(I)CP*CP*GP*G)-3 T4 lysozyme mutant - S32A hen egg white lysozyme at -30 degrees C quail egg white lysozyme at 2 atmospheres This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the STRUCT_ASYM category record details about the structural elements in the asymmetric unit. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:struct_asymCategory> <PDBx:struct_asym id="A"> <PDBx:entity_id>1</PDBx:entity_id> <PDBx:details>one monomer of the dimeric enzyme</PDBx:details> </PDBx:struct_asym> <PDBx:struct_asym id="B"> <PDBx:entity_id>1</PDBx:entity_id> <PDBx:details>one monomer of the dimeric enzyme</PDBx:details> </PDBx:struct_asym> <PDBx:struct_asym id="C"> <PDBx:entity_id>2</PDBx:entity_id> <PDBx:details>one partially occupied position for the inhibitor</PDBx:details> </PDBx:struct_asym> <PDBx:struct_asym id="D"> <PDBx:entity_id>2</PDBx:entity_id> <PDBx:details>one partially occupied position for the inhibitor</PDBx:details> </PDBx:struct_asym> </PDBx:struct_asymCategory> A description of special aspects of this portion of the contents of the asymmetric unit. The drug binds to this enzyme in two roughly twofold symmetric modes. Hence this biological unit (3) is roughly twofold symmetric to biological unit (2). Disorder in the protein chain indicated with alternative id 2 should be used with this biological unit. This data item is a pointer to attribute id in category entity in the ENTITY category. A flag indicating that this entity was originally labeled with a blank PDB chain id. This data item indicates whether the structural elements are modified. y The value of attribute id in category struct_asym must uniquely identify a record in the STRUCT_ASYM list. Note that this item need not be a number; it can be any unique identifier. 1 A 2B3 Data items in the STRUCT_BIOL category record details about the structural elements that form each structure of biological significance. A given crystal structure may contain many different biological structures. A given structural component in the asymmetric unit may be part of more than one biological unit. A given biological structure may involve crystallographic symmetry. For instance, in a structure of a lysozyme-FAB structure, the light and heavy chain components of the FAB could be one biological unit, while the two chains of the FAB and the lysozyme could constitute a second biological unit. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:struct_biolCategory> <PDBx:struct_biol id="1"> <PDBx:details> significant deviations from twofold symmetry exist in this dimeric enzyme</PDBx:details> </PDBx:struct_biol> <PDBx:struct_biol id="2"> <PDBx:details> The drug binds to this enzyme in two roughly twofold symmetric modes. Hence this biological unit (2) is roughly twofold symmetric to biological unit (3). Disorder in the protein chain indicated with alternative id 1 should be used with this biological unit.</PDBx:details> </PDBx:struct_biol> <PDBx:struct_biol id="3"> <PDBx:details> The drug binds to this enzyme in two roughly twofold symmetric modes. Hence this biological unit (3) is roughly twofold symmetric to biological unit (2). Disorder in the protein chain indicated with alternative id 2 should be used with this biological unit.</PDBx:details> </PDBx:struct_biol> </PDBx:struct_biolCategory>