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 <RCSB:atom_siteCategory> <RCSB:atom_site id="1"> <RCSB:group_PDB>ATOM</RCSB:group_PDB> <RCSB:type_symbol>N</RCSB:type_symbol> <RCSB:label_atom_id>N</RCSB:label_atom_id> <RCSB:label_comp_id>VAL</RCSB:label_comp_id> <RCSB:label_asym_id>A</RCSB:label_asym_id> <RCSB:label_seq_id>11</RCSB:label_seq_id> <RCSB:label_alt_id xsi:nil="true" /> <RCSB:Cartn_x>25.369</RCSB:Cartn_x> <RCSB:Cartn_y>30.691</RCSB:Cartn_y> <RCSB:Cartn_z>11.795</RCSB:Cartn_z> <RCSB:occupancy>1.00</RCSB:occupancy> <RCSB:B_iso_or_equiv>17.93</RCSB:B_iso_or_equiv> <RCSB:auth_seq_id>11</RCSB:auth_seq_id> </RCSB:atom_site> <RCSB:atom_site id="2"> <RCSB:group_PDB>ATOM</RCSB:group_PDB> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:label_atom_id>CA</RCSB:label_atom_id> <RCSB:label_comp_id>VAL</RCSB:label_comp_id> <RCSB:label_asym_id>A</RCSB:label_asym_id> <RCSB:label_seq_id>11</RCSB:label_seq_id> <RCSB:label_alt_id xsi:nil="true" /> <RCSB:Cartn_x>25.970</RCSB:Cartn_x> <RCSB:Cartn_y>31.965</RCSB:Cartn_y> <RCSB:Cartn_z>12.332</RCSB:Cartn_z> <RCSB:occupancy>1.00</RCSB:occupancy> <RCSB:B_iso_or_equiv>17.75</RCSB:B_iso_or_equiv> <RCSB:auth_seq_id>11</RCSB:auth_seq_id> </RCSB:atom_site> <RCSB:atom_site id="3"> <RCSB:group_PDB>ATOM</RCSB:group_PDB> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:label_atom_id>C</RCSB:label_atom_id> <RCSB:label_comp_id>VAL</RCSB:label_comp_id> <RCSB:label_asym_id>A</RCSB:label_asym_id> <RCSB:label_seq_id>11</RCSB:label_seq_id> <RCSB:label_alt_id xsi:nil="true" /> <RCSB:Cartn_x>25.569</RCSB:Cartn_x> <RCSB:Cartn_y>32.010</RCSB:Cartn_y> <RCSB:Cartn_z>13.808</RCSB:Cartn_z> <RCSB:occupancy>1.00</RCSB:occupancy> <RCSB:B_iso_or_equiv>17.83</RCSB:B_iso_or_equiv> <RCSB:auth_seq_id>11</RCSB:auth_seq_id> </RCSB:atom_site> <RCSB:atom_site id="4"> <RCSB:group_PDB>ATOM</RCSB:group_PDB> <RCSB:type_symbol>O</RCSB:type_symbol> <RCSB:label_atom_id>O</RCSB:label_atom_id> <RCSB:label_comp_id>VAL</RCSB:label_comp_id> <RCSB:label_asym_id>A</RCSB:label_asym_id> <RCSB:label_seq_id>11</RCSB:label_seq_id> <RCSB:label_alt_id xsi:nil="true" /> <RCSB:Cartn_x>24.735</RCSB:Cartn_x> <RCSB:Cartn_y>31.190</RCSB:Cartn_y> <RCSB:Cartn_z>14.167</RCSB:Cartn_z> <RCSB:occupancy>1.00</RCSB:occupancy> <RCSB:B_iso_or_equiv>17.53</RCSB:B_iso_or_equiv> <RCSB:auth_seq_id>11</RCSB:auth_seq_id> </RCSB:atom_site> <RCSB:atom_site id="5"> <RCSB:group_PDB>ATOM</RCSB:group_PDB> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:label_atom_id>CB</RCSB:label_atom_id> <RCSB:label_comp_id>VAL</RCSB:label_comp_id> <RCSB:label_asym_id>A</RCSB:label_asym_id> <RCSB:label_seq_id>11</RCSB:label_seq_id> <RCSB:label_alt_id xsi:nil="true" /> <RCSB:Cartn_x>25.379</RCSB:Cartn_x> <RCSB:Cartn_y>33.146</RCSB:Cartn_y> <RCSB:Cartn_z>11.540</RCSB:Cartn_z> <RCSB:occupancy>1.00</RCSB:occupancy> <RCSB:B_iso_or_equiv>17.66</RCSB:B_iso_or_equiv> <RCSB:auth_seq_id>11</RCSB:auth_seq_id> </RCSB:atom_site> <RCSB:atom_site id="6"> <RCSB:group_PDB>ATOM</RCSB:group_PDB> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:label_atom_id>CG1</RCSB:label_atom_id> <RCSB:label_comp_id>VAL</RCSB:label_comp_id> <RCSB:label_asym_id>A</RCSB:label_asym_id> <RCSB:label_seq_id>11</RCSB:label_seq_id> <RCSB:label_alt_id xsi:nil="true" /> <RCSB:Cartn_x>25.584</RCSB:Cartn_x> <RCSB:Cartn_y>33.034</RCSB:Cartn_y> <RCSB:Cartn_z>10.030</RCSB:Cartn_z> <RCSB:occupancy>1.00</RCSB:occupancy> <RCSB:B_iso_or_equiv>18.86</RCSB:B_iso_or_equiv> <RCSB:auth_seq_id>11</RCSB:auth_seq_id> </RCSB:atom_site> <RCSB:atom_site id="7"> <RCSB:group_PDB>ATOM</RCSB:group_PDB> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:label_atom_id>CG2</RCSB:label_atom_id> <RCSB:label_comp_id>VAL</RCSB:label_comp_id> <RCSB:label_asym_id>A</RCSB:label_asym_id> <RCSB:label_seq_id>11</RCSB:label_seq_id> <RCSB:label_alt_id xsi:nil="true" /> <RCSB:Cartn_x>23.933</RCSB:Cartn_x> <RCSB:Cartn_y>33.309</RCSB:Cartn_y> <RCSB:Cartn_z>11.872</RCSB:Cartn_z> <RCSB:occupancy>1.00</RCSB:occupancy> <RCSB:B_iso_or_equiv>17.12</RCSB:B_iso_or_equiv> <RCSB:auth_seq_id>11</RCSB:auth_seq_id> </RCSB:atom_site> <RCSB:atom_site id="8"> <RCSB:group_PDB>ATOM</RCSB:group_PDB> <RCSB:type_symbol>N</RCSB:type_symbol> <RCSB:label_atom_id>N</RCSB:label_atom_id> <RCSB:label_comp_id>THR</RCSB:label_comp_id> <RCSB:label_asym_id>A</RCSB:label_asym_id> <RCSB:label_seq_id>12</RCSB:label_seq_id> <RCSB:label_alt_id xsi:nil="true" /> <RCSB:Cartn_x>26.095</RCSB:Cartn_x> <RCSB:Cartn_y>32.930</RCSB:Cartn_y> <RCSB:Cartn_z>14.590</RCSB:Cartn_z> <RCSB:occupancy>1.00</RCSB:occupancy> <RCSB:B_iso_or_equiv>18.97</RCSB:B_iso_or_equiv> <RCSB:footnote_id>4</RCSB:footnote_id> <RCSB:auth_seq_id>12</RCSB:auth_seq_id> </RCSB:atom_site> <RCSB:atom_site id="9"> <RCSB:group_PDB>ATOM</RCSB:group_PDB> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:label_atom_id>CA</RCSB:label_atom_id> <RCSB:label_comp_id>THR</RCSB:label_comp_id> <RCSB:label_asym_id>A</RCSB:label_asym_id> <RCSB:label_seq_id>12</RCSB:label_seq_id> <RCSB:label_alt_id xsi:nil="true" /> <RCSB:Cartn_x>25.734</RCSB:Cartn_x> <RCSB:Cartn_y>32.995</RCSB:Cartn_y> <RCSB:Cartn_z>16.032</RCSB:Cartn_z> <RCSB:occupancy>1.00</RCSB:occupancy> <RCSB:B_iso_or_equiv>19.80</RCSB:B_iso_or_equiv> <RCSB:footnote_id>4</RCSB:footnote_id> <RCSB:auth_seq_id>12</RCSB:auth_seq_id> </RCSB:atom_site> <RCSB:atom_site id="10"> <RCSB:group_PDB>ATOM</RCSB:group_PDB> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:label_atom_id>C</RCSB:label_atom_id> <RCSB:label_comp_id>THR</RCSB:label_comp_id> <RCSB:label_asym_id>A</RCSB:label_asym_id> <RCSB:label_seq_id>12</RCSB:label_seq_id> <RCSB:label_alt_id xsi:nil="true" /> <RCSB:Cartn_x>24.695</RCSB:Cartn_x> <RCSB:Cartn_y>34.106</RCSB:Cartn_y> <RCSB:Cartn_z>16.113</RCSB:Cartn_z> <RCSB:occupancy>1.00</RCSB:occupancy> <RCSB:B_iso_or_equiv>20.92</RCSB:B_iso_or_equiv> <RCSB:footnote_id>4</RCSB:footnote_id> <RCSB:auth_seq_id>12</RCSB:auth_seq_id> </RCSB:atom_site> <RCSB:atom_site id="11"> <RCSB:group_PDB>ATOM</RCSB:group_PDB> <RCSB:type_symbol>O</RCSB:type_symbol> <RCSB:label_atom_id>O</RCSB:label_atom_id> <RCSB:label_comp_id>THR</RCSB:label_comp_id> <RCSB:label_asym_id>A</RCSB:label_asym_id> <RCSB:label_seq_id>12</RCSB:label_seq_id> <RCSB:label_alt_id xsi:nil="true" /> <RCSB:Cartn_x>24.869</RCSB:Cartn_x> <RCSB:Cartn_y>35.118</RCSB:Cartn_y> <RCSB:Cartn_z>15.421</RCSB:Cartn_z> <RCSB:occupancy>1.00</RCSB:occupancy> <RCSB:B_iso_or_equiv>21.84</RCSB:B_iso_or_equiv> <RCSB:footnote_id>4</RCSB:footnote_id> <RCSB:auth_seq_id>12</RCSB:auth_seq_id> </RCSB:atom_site> <RCSB:atom_site id="12"> <RCSB:group_PDB>ATOM</RCSB:group_PDB> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:label_atom_id>CB</RCSB:label_atom_id> <RCSB:label_comp_id>THR</RCSB:label_comp_id> <RCSB:label_asym_id>A</RCSB:label_asym_id> <RCSB:label_seq_id>12</RCSB:label_seq_id> <RCSB:label_alt_id xsi:nil="true" /> <RCSB:Cartn_x>26.911</RCSB:Cartn_x> <RCSB:Cartn_y>33.346</RCSB:Cartn_y> <RCSB:Cartn_z>17.018</RCSB:Cartn_z> <RCSB:occupancy>1.00</RCSB:occupancy> <RCSB:B_iso_or_equiv>20.51</RCSB:B_iso_or_equiv> <RCSB:footnote_id>4</RCSB:footnote_id> <RCSB:auth_seq_id>12</RCSB:auth_seq_id> </RCSB:atom_site> <RCSB:atom_site id="13"> <RCSB:group_PDB>ATOM</RCSB:group_PDB> <RCSB:type_symbol>O</RCSB:type_symbol> <RCSB:label_atom_id>OG1</RCSB:label_atom_id> <RCSB:label_comp_id>THR</RCSB:label_comp_id> <RCSB:label_asym_id>A</RCSB:label_asym_id> <RCSB:label_seq_id>12</RCSB:label_seq_id> <RCSB:label_alt_id>3</RCSB:label_alt_id> <RCSB:Cartn_x>27.946</RCSB:Cartn_x> <RCSB:Cartn_y>33.921</RCSB:Cartn_y> <RCSB:Cartn_z>16.183</RCSB:Cartn_z> <RCSB:occupancy>0.50</RCSB:occupancy> <RCSB:B_iso_or_equiv>20.29</RCSB:B_iso_or_equiv> <RCSB:footnote_id>4</RCSB:footnote_id> <RCSB:auth_seq_id>12</RCSB:auth_seq_id> </RCSB:atom_site> <RCSB:atom_site id="14"> <RCSB:group_PDB>ATOM</RCSB:group_PDB> <RCSB:type_symbol>O</RCSB:type_symbol> <RCSB:label_atom_id>OG1</RCSB:label_atom_id> <RCSB:label_comp_id>THR</RCSB:label_comp_id> <RCSB:label_asym_id>A</RCSB:label_asym_id> <RCSB:label_seq_id>12</RCSB:label_seq_id> <RCSB:label_alt_id>4</RCSB:label_alt_id> <RCSB:Cartn_x>27.769</RCSB:Cartn_x> <RCSB:Cartn_y>32.142</RCSB:Cartn_y> <RCSB:Cartn_z>17.103</RCSB:Cartn_z> <RCSB:occupancy>0.50</RCSB:occupancy> <RCSB:B_iso_or_equiv>20.59</RCSB:B_iso_or_equiv> <RCSB:footnote_id>4</RCSB:footnote_id> <RCSB:auth_seq_id>12</RCSB:auth_seq_id> </RCSB:atom_site> <RCSB:atom_site id="15"> <RCSB:group_PDB>ATOM</RCSB:group_PDB> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:label_atom_id>CG2</RCSB:label_atom_id> <RCSB:label_comp_id>THR</RCSB:label_comp_id> <RCSB:label_asym_id>A</RCSB:label_asym_id> <RCSB:label_seq_id>12</RCSB:label_seq_id> <RCSB:label_alt_id>3</RCSB:label_alt_id> <RCSB:Cartn_x>27.418</RCSB:Cartn_x> <RCSB:Cartn_y>32.181</RCSB:Cartn_y> <RCSB:Cartn_z>17.878</RCSB:Cartn_z> <RCSB:occupancy>0.50</RCSB:occupancy> <RCSB:B_iso_or_equiv>20.47</RCSB:B_iso_or_equiv> <RCSB:footnote_id>4</RCSB:footnote_id> <RCSB:auth_seq_id>12</RCSB:auth_seq_id> </RCSB:atom_site> <RCSB:atom_site id="16"> <RCSB:group_PDB>ATOM</RCSB:group_PDB> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:label_atom_id>CG2</RCSB:label_atom_id> <RCSB:label_comp_id>THR</RCSB:label_comp_id> <RCSB:label_asym_id>A</RCSB:label_asym_id> <RCSB:label_seq_id>12</RCSB:label_seq_id> <RCSB:label_alt_id>4</RCSB:label_alt_id> <RCSB:Cartn_x>26.489</RCSB:Cartn_x> <RCSB:Cartn_y>33.778</RCSB:Cartn_y> <RCSB:Cartn_z>18.426</RCSB:Cartn_z> <RCSB:occupancy>0.50</RCSB:occupancy> <RCSB:B_iso_or_equiv>20.00</RCSB:B_iso_or_equiv> <RCSB:footnote_id>4</RCSB:footnote_id> <RCSB:auth_seq_id>12</RCSB:auth_seq_id> </RCSB:atom_site> <RCSB:atom_site id="17"> <RCSB:group_PDB>ATOM</RCSB:group_PDB> <RCSB:type_symbol>N</RCSB:type_symbol> <RCSB:label_atom_id>N</RCSB:label_atom_id> <RCSB:label_comp_id>ILE</RCSB:label_comp_id> <RCSB:label_asym_id>A</RCSB:label_asym_id> <RCSB:label_seq_id>13</RCSB:label_seq_id> <RCSB:label_alt_id xsi:nil="true" /> <RCSB:Cartn_x>23.664</RCSB:Cartn_x> <RCSB:Cartn_y>33.855</RCSB:Cartn_y> <RCSB:Cartn_z>16.884</RCSB:Cartn_z> <RCSB:occupancy>1.00</RCSB:occupancy> <RCSB:B_iso_or_equiv>22.08</RCSB:B_iso_or_equiv> <RCSB:auth_seq_id>13</RCSB:auth_seq_id> </RCSB:atom_site> <RCSB:atom_site id="18"> <RCSB:group_PDB>ATOM</RCSB:group_PDB> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:label_atom_id>CA</RCSB:label_atom_id> <RCSB:label_comp_id>ILE</RCSB:label_comp_id> <RCSB:label_asym_id>A</RCSB:label_asym_id> <RCSB:label_seq_id>13</RCSB:label_seq_id> <RCSB:label_alt_id xsi:nil="true" /> <RCSB:Cartn_x>22.623</RCSB:Cartn_x> <RCSB:Cartn_y>34.850</RCSB:Cartn_y> <RCSB:Cartn_z>17.093</RCSB:Cartn_z> <RCSB:occupancy>1.00</RCSB:occupancy> <RCSB:B_iso_or_equiv>23.44</RCSB:B_iso_or_equiv> <RCSB:auth_seq_id>13</RCSB:auth_seq_id> </RCSB:atom_site> <RCSB:atom_site id="19"> <RCSB:group_PDB>ATOM</RCSB:group_PDB> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:label_atom_id>C</RCSB:label_atom_id> <RCSB:label_comp_id>ILE</RCSB:label_comp_id> <RCSB:label_asym_id>A</RCSB:label_asym_id> <RCSB:label_seq_id>13</RCSB:label_seq_id> <RCSB:label_alt_id xsi:nil="true" /> <RCSB:Cartn_x>22.657</RCSB:Cartn_x> <RCSB:Cartn_y>35.113</RCSB:Cartn_y> <RCSB:Cartn_z>18.610</RCSB:Cartn_z> <RCSB:occupancy>1.00</RCSB:occupancy> <RCSB:B_iso_or_equiv>25.77</RCSB:B_iso_or_equiv> <RCSB:auth_seq_id>13</RCSB:auth_seq_id> </RCSB:atom_site> <RCSB:atom_site id="20"> <RCSB:group_PDB>ATOM</RCSB:group_PDB> <RCSB:type_symbol>O</RCSB:type_symbol> <RCSB:label_atom_id>O</RCSB:label_atom_id> <RCSB:label_comp_id>ILE</RCSB:label_comp_id> <RCSB:label_asym_id>A</RCSB:label_asym_id> <RCSB:label_seq_id>13</RCSB:label_seq_id> <RCSB:label_alt_id xsi:nil="true" /> <RCSB:Cartn_x>23.123</RCSB:Cartn_x> <RCSB:Cartn_y>34.250</RCSB:Cartn_y> <RCSB:Cartn_z>19.406</RCSB:Cartn_z> <RCSB:occupancy>1.00</RCSB:occupancy> <RCSB:B_iso_or_equiv>26.28</RCSB:B_iso_or_equiv> <RCSB:auth_seq_id>13</RCSB:auth_seq_id> </RCSB:atom_site> <RCSB:atom_site id="21"> <RCSB:group_PDB>ATOM</RCSB:group_PDB> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:label_atom_id>CB</RCSB:label_atom_id> <RCSB:label_comp_id>ILE</RCSB:label_comp_id> <RCSB:label_asym_id>A</RCSB:label_asym_id> <RCSB:label_seq_id>13</RCSB:label_seq_id> <RCSB:label_alt_id xsi:nil="true" /> <RCSB:Cartn_x>21.236</RCSB:Cartn_x> <RCSB:Cartn_y>34.463</RCSB:Cartn_y> <RCSB:Cartn_z>16.492</RCSB:Cartn_z> <RCSB:occupancy>1.00</RCSB:occupancy> <RCSB:B_iso_or_equiv>22.67</RCSB:B_iso_or_equiv> <RCSB:auth_seq_id>13</RCSB:auth_seq_id> </RCSB:atom_site> <RCSB:atom_site id="22"> <RCSB:group_PDB>ATOM</RCSB:group_PDB> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:label_atom_id>CG1</RCSB:label_atom_id> <RCSB:label_comp_id>ILE</RCSB:label_comp_id> <RCSB:label_asym_id>A</RCSB:label_asym_id> <RCSB:label_seq_id>13</RCSB:label_seq_id> <RCSB:label_alt_id xsi:nil="true" /> <RCSB:Cartn_x>20.478</RCSB:Cartn_x> <RCSB:Cartn_y>33.469</RCSB:Cartn_y> <RCSB:Cartn_z>17.371</RCSB:Cartn_z> <RCSB:occupancy>1.00</RCSB:occupancy> <RCSB:B_iso_or_equiv>22.14</RCSB:B_iso_or_equiv> <RCSB:auth_seq_id>13</RCSB:auth_seq_id> </RCSB:atom_site> <RCSB:atom_site id="23"> <RCSB:group_PDB>ATOM</RCSB:group_PDB> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:label_atom_id>CG2</RCSB:label_atom_id> <RCSB:label_comp_id>ILE</RCSB:label_comp_id> <RCSB:label_asym_id>A</RCSB:label_asym_id> <RCSB:label_seq_id>13</RCSB:label_seq_id> <RCSB:label_alt_id xsi:nil="true" /> <RCSB:Cartn_x>21.357</RCSB:Cartn_x> <RCSB:Cartn_y>33.986</RCSB:Cartn_y> <RCSB:Cartn_z>15.016</RCSB:Cartn_z> <RCSB:occupancy>1.00</RCSB:occupancy> <RCSB:B_iso_or_equiv>21.75</RCSB:B_iso_or_equiv> <RCSB:auth_seq_id>13</RCSB:auth_seq_id> </RCSB:atom_site> <RCSB:atom_site id="101"> <RCSB:group_PDB>HETATM</RCSB:group_PDB> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:label_atom_id>C1</RCSB:label_atom_id> <RCSB:label_comp_id>APS</RCSB:label_comp_id> <RCSB:label_asym_id>C</RCSB:label_asym_id> <RCSB:label_seq_id xsi:nil="true" /> <RCSB:label_alt_id>1</RCSB:label_alt_id> <RCSB:Cartn_x>4.171</RCSB:Cartn_x> <RCSB:Cartn_y>29.012</RCSB:Cartn_y> <RCSB:Cartn_z>7.116</RCSB:Cartn_z> <RCSB:occupancy>0.58</RCSB:occupancy> <RCSB:B_iso_or_equiv>17.27</RCSB:B_iso_or_equiv> <RCSB:footnote_id>1</RCSB:footnote_id> <RCSB:auth_seq_id>300</RCSB:auth_seq_id> </RCSB:atom_site> <RCSB:atom_site id="102"> <RCSB:group_PDB>HETATM</RCSB:group_PDB> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:label_atom_id>C2</RCSB:label_atom_id> <RCSB:label_comp_id>APS</RCSB:label_comp_id> <RCSB:label_asym_id>C</RCSB:label_asym_id> <RCSB:label_seq_id xsi:nil="true" /> <RCSB:label_alt_id>1</RCSB:label_alt_id> <RCSB:Cartn_x>4.949</RCSB:Cartn_x> <RCSB:Cartn_y>27.758</RCSB:Cartn_y> <RCSB:Cartn_z>6.793</RCSB:Cartn_z> <RCSB:occupancy>0.58</RCSB:occupancy> <RCSB:B_iso_or_equiv>16.95</RCSB:B_iso_or_equiv> <RCSB:footnote_id>1</RCSB:footnote_id> <RCSB:auth_seq_id>300</RCSB:auth_seq_id> </RCSB:atom_site> <RCSB:atom_site id="103"> <RCSB:group_PDB>HETATM</RCSB:group_PDB> <RCSB:type_symbol>O</RCSB:type_symbol> <RCSB:label_atom_id>O3</RCSB:label_atom_id> <RCSB:label_comp_id>APS</RCSB:label_comp_id> <RCSB:label_asym_id>C</RCSB:label_asym_id> <RCSB:label_seq_id xsi:nil="true" /> <RCSB:label_alt_id>1</RCSB:label_alt_id> <RCSB:Cartn_x>4.800</RCSB:Cartn_x> <RCSB:Cartn_y>26.678</RCSB:Cartn_y> <RCSB:Cartn_z>7.393</RCSB:Cartn_z> <RCSB:occupancy>0.58</RCSB:occupancy> <RCSB:B_iso_or_equiv>16.85</RCSB:B_iso_or_equiv> <RCSB:footnote_id>1</RCSB:footnote_id> <RCSB:auth_seq_id>300</RCSB:auth_seq_id> </RCSB:atom_site> <RCSB:atom_site id="104"> <RCSB:group_PDB>HETATM</RCSB:group_PDB> <RCSB:type_symbol>N</RCSB:type_symbol> <RCSB:label_atom_id>N4</RCSB:label_atom_id> <RCSB:label_comp_id>APS</RCSB:label_comp_id> <RCSB:label_asym_id>C</RCSB:label_asym_id> <RCSB:label_seq_id xsi:nil="true" /> <RCSB:label_alt_id>1</RCSB:label_alt_id> <RCSB:Cartn_x>5.930</RCSB:Cartn_x> <RCSB:Cartn_y>27.841</RCSB:Cartn_y> <RCSB:Cartn_z>5.869</RCSB:Cartn_z> <RCSB:occupancy>0.58</RCSB:occupancy> <RCSB:B_iso_or_equiv>16.43</RCSB:B_iso_or_equiv> <RCSB:footnote_id>1</RCSB:footnote_id> <RCSB:auth_seq_id>300</RCSB:auth_seq_id> </RCSB:atom_site> </RCSB: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. PDB atom name. PDB residue name. PDB residue number. PDB strand id. Author's alternate location identifier Author's strand id. Author's atom name. Author's residue name. Author's sequence identifier. Placeholder for PDB insertion code. Sequential residue number used by NDB. Will identify with a 'Y' that this strand got generated. 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. 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]. <RCSB:atom_site_anisotropCategory> <RCSB:atom_site_anisotrop id="1"> <RCSB:type_symbol>O</RCSB:type_symbol> <RCSB:U11>8642.</RCSB:U11> <RCSB:U12>4866.</RCSB:U12> <RCSB:U13>7299.</RCSB:U13> <RCSB:U22>-342.</RCSB:U22> <RCSB:U23>-258.</RCSB:U23> <RCSB:U33>-1427.</RCSB:U33> </RCSB:atom_site_anisotrop> <RCSB:atom_site_anisotrop id="2"> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:U11>5174.</RCSB:U11> <RCSB:U12>4871.</RCSB:U12> <RCSB:U13>6243.</RCSB:U13> <RCSB:U22>-1885.</RCSB:U22> <RCSB:U23>-2051.</RCSB:U23> <RCSB:U33>-1377.</RCSB:U33> </RCSB:atom_site_anisotrop> <RCSB:atom_site_anisotrop id="3"> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:U11>6202.</RCSB:U11> <RCSB:U12>5020.</RCSB:U12> <RCSB:U13>4395.</RCSB:U13> <RCSB:U22>-1130.</RCSB:U22> <RCSB:U23>-556.</RCSB:U23> <RCSB:U33>-632.</RCSB:U33> </RCSB:atom_site_anisotrop> <RCSB:atom_site_anisotrop id="4"> <RCSB:type_symbol>O</RCSB:type_symbol> <RCSB:U11>4224.</RCSB:U11> <RCSB:U12>4700.</RCSB:U12> <RCSB:U13>5046.</RCSB:U13> <RCSB:U22>1105.</RCSB:U22> <RCSB:U23>-161.</RCSB:U23> <RCSB:U33>345.</RCSB:U33> </RCSB:atom_site_anisotrop> <RCSB:atom_site_anisotrop id="5"> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:U11>8684.</RCSB:U11> <RCSB:U12>4688.</RCSB:U12> <RCSB:U13>4171.</RCSB:U13> <RCSB:U22>-1850.</RCSB:U22> <RCSB:U23>-433.</RCSB:U23> <RCSB:U33>-292.</RCSB:U33> </RCSB:atom_site_anisotrop> <RCSB:atom_site_anisotrop id="6"> <RCSB:type_symbol>O</RCSB:type_symbol> <RCSB:U11>11226.</RCSB:U11> <RCSB:U12>5255.</RCSB:U12> <RCSB:U13>3532.</RCSB:U13> <RCSB:U22>-341.</RCSB:U22> <RCSB:U23>2685.</RCSB:U23> <RCSB:U33>1328.</RCSB:U33> </RCSB:atom_site_anisotrop> <RCSB:atom_site_anisotrop id="7"> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:U11>10214.</RCSB:U11> <RCSB:U12>2428.</RCSB:U12> <RCSB:U13>5614.</RCSB:U13> <RCSB:U22>-2610.</RCSB:U22> <RCSB:U23>-1940.</RCSB:U23> <RCSB:U33>902.</RCSB:U33> </RCSB:atom_site_anisotrop> <RCSB:atom_site_anisotrop id="8"> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:U11>4590.</RCSB:U11> <RCSB:U12>3488.</RCSB:U12> <RCSB:U13>5827.</RCSB:U13> <RCSB:U22>751.</RCSB:U22> <RCSB:U23>-770.</RCSB:U23> <RCSB:U33>986.</RCSB:U33> </RCSB:atom_site_anisotrop> <RCSB:atom_site_anisotrop id="9"> <RCSB:type_symbol>N</RCSB:type_symbol> <RCSB:U11>5014.</RCSB:U11> <RCSB:U12>4434.</RCSB:U12> <RCSB:U13>3447.</RCSB:U13> <RCSB:U22>-17.</RCSB:U22> <RCSB:U23>-1593.</RCSB:U23> <RCSB:U33>539.</RCSB:U33> </RCSB:atom_site_anisotrop> </RCSB: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. PDB atom name. PDB residue name. PDB residue number. PDB strand id. Author's strand id. Author's atom name. Author's residue name. NDB sequence ID. NDB ALT ID. NDB ASYM ID. NDB ATOM ID NDB COMP ID NDB INSERTION CODE Sequential residue number used by NDB. Will identify with a 'Y' that this strand got generated. 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 <RCSB:atom_sitesCategory> <RCSB:atom_sites entry_id="5HVP"> <RCSB:Cartn_transform_axes>c along z, astar along x, b along y</RCSB:Cartn_transform_axes> <RCSB:Cartn_transf_matrix11>58.39</RCSB:Cartn_transf_matrix11> <RCSB:Cartn_transf_matrix12>0.00</RCSB:Cartn_transf_matrix12> <RCSB:Cartn_transf_matrix13>0.00</RCSB:Cartn_transf_matrix13> <RCSB:Cartn_transf_matrix21>0.00</RCSB:Cartn_transf_matrix21> <RCSB:Cartn_transf_matrix22>86.70</RCSB:Cartn_transf_matrix22> <RCSB:Cartn_transf_matrix23>0.00</RCSB:Cartn_transf_matrix23> <RCSB:Cartn_transf_matrix31>0.00</RCSB:Cartn_transf_matrix31> <RCSB:Cartn_transf_matrix32>0.00</RCSB:Cartn_transf_matrix32> <RCSB:Cartn_transf_matrix33>46.27</RCSB:Cartn_transf_matrix33> <RCSB:Cartn_transf_vector1>0.00</RCSB:Cartn_transf_vector1> <RCSB:Cartn_transf_vector2>0.00</RCSB:Cartn_transf_vector2> <RCSB:Cartn_transf_vector3>0.00</RCSB:Cartn_transf_vector3> </RCSB:atom_sites> </RCSB: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 <RCSB:atom_sites_altCategory> <RCSB:atom_sites_alt id=""> <RCSB:details> Atom sites with the alternative id set to null are not modeled in alternative conformations</RCSB:details> </RCSB:atom_sites_alt> <RCSB:atom_sites_alt id="1"> <RCSB: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.</RCSB:details> </RCSB:atom_sites_alt> <RCSB:atom_sites_alt id="2"> <RCSB: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.</RCSB:details> </RCSB:atom_sites_alt> <RCSB:atom_sites_alt id="3"> <RCSB: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.</RCSB:details> </RCSB:atom_sites_alt> <RCSB:atom_sites_alt id="4"> <RCSB: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.</RCSB:details> </RCSB:atom_sites_alt> </RCSB: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 <RCSB:atom_sites_alt_ensCategory> <RCSB:atom_sites_alt_ens id="Ensemble 1-A"> <RCSB: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.</RCSB:details> </RCSB:atom_sites_alt_ens> <RCSB:atom_sites_alt_ens id="Ensemble 1-B"> <RCSB: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.</RCSB:details> </RCSB:atom_sites_alt_ens> <RCSB:atom_sites_alt_ens id="Ensemble 2-A"> <RCSB: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.</RCSB:details> </RCSB:atom_sites_alt_ens> <RCSB:atom_sites_alt_ens id="Ensemble 2-B"> <RCSB: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.</RCSB:details> </RCSB:atom_sites_alt_ens> </RCSB: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 <RCSB:atom_sites_alt_genCategory> <RCSB:atom_sites_alt_gen ens_id="Ensemble 1-A" alt_id=""></RCSB:atom_sites_alt_gen> <RCSB:atom_sites_alt_gen ens_id="Ensemble 1-A" alt_id="1"></RCSB:atom_sites_alt_gen> <RCSB:atom_sites_alt_gen ens_id="Ensemble 1-A" alt_id="3"></RCSB:atom_sites_alt_gen> <RCSB:atom_sites_alt_gen ens_id="Ensemble 1-B" alt_id=""></RCSB:atom_sites_alt_gen> <RCSB:atom_sites_alt_gen ens_id="Ensemble 1-B" alt_id="1"></RCSB:atom_sites_alt_gen> <RCSB:atom_sites_alt_gen ens_id="Ensemble 1-B" alt_id="4"></RCSB:atom_sites_alt_gen> <RCSB:atom_sites_alt_gen ens_id="Ensemble 2-A" alt_id=""></RCSB:atom_sites_alt_gen> <RCSB:atom_sites_alt_gen ens_id="Ensemble 2-A" alt_id="2"></RCSB:atom_sites_alt_gen> <RCSB:atom_sites_alt_gen ens_id="Ensemble 2-A" alt_id="3"></RCSB:atom_sites_alt_gen> <RCSB:atom_sites_alt_gen ens_id="Ensemble 2-B" alt_id=""></RCSB:atom_sites_alt_gen> <RCSB:atom_sites_alt_gen ens_id="Ensemble 2-B" alt_id="2"></RCSB:atom_sites_alt_gen> <RCSB:atom_sites_alt_gen ens_id="Ensemble 2-B" alt_id="4"></RCSB:atom_sites_alt_gen> </RCSB: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 <RCSB:atom_sites_footnoteCategory> <RCSB:atom_sites_footnote id="1"> <RCSB:text> The inhibitor binds to the enzyme in two alternative orientations. The two orientations have been assigned alternative ids *1* and *2*.</RCSB:text> </RCSB:atom_sites_footnote> <RCSB:atom_sites_footnote id="2"> <RCSB: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*.</RCSB:text> </RCSB:atom_sites_footnote> <RCSB:atom_sites_footnote id="3"> <RCSB: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*.</RCSB:text> </RCSB:atom_sites_footnote> <RCSB:atom_sites_footnote id="4"> <RCSB:text> Side chains of these residues adopt alternative orientations that do not correlate with the alternative orientation of the inhibitor. </RCSB:text> </RCSB:atom_sites_footnote> <RCSB:atom_sites_footnote id="5"> <RCSB: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.</RCSB:text> </RCSB:atom_sites_footnote> </RCSB: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 <RCSB:atom_typeCategory> <RCSB:atom_type symbol="C"> <RCSB:oxidation_number>0</RCSB:oxidation_number> <RCSB:scat_Cromer_Mann_a1>2.31000</RCSB:scat_Cromer_Mann_a1> <RCSB:scat_Cromer_Mann_a2>20.8439</RCSB:scat_Cromer_Mann_a2> <RCSB:scat_Cromer_Mann_a3>1.02000</RCSB:scat_Cromer_Mann_a3> <RCSB:scat_Cromer_Mann_a4>10.2075</RCSB:scat_Cromer_Mann_a4> <RCSB:scat_Cromer_Mann_b1>1.58860</RCSB:scat_Cromer_Mann_b1> <RCSB:scat_Cromer_Mann_b2>0.568700</RCSB:scat_Cromer_Mann_b2> <RCSB:scat_Cromer_Mann_b3>0.865000</RCSB:scat_Cromer_Mann_b3> <RCSB:scat_Cromer_Mann_b4>51.6512</RCSB:scat_Cromer_Mann_b4> <RCSB:scat_Cromer_Mann_c>0.21560</RCSB:scat_Cromer_Mann_c> </RCSB:atom_type> <RCSB:atom_type symbol="N"> <RCSB:oxidation_number>0</RCSB:oxidation_number> <RCSB:scat_Cromer_Mann_a1>12.2126</RCSB:scat_Cromer_Mann_a1> <RCSB:scat_Cromer_Mann_a2>0.005700</RCSB:scat_Cromer_Mann_a2> <RCSB:scat_Cromer_Mann_a3>3.13220</RCSB:scat_Cromer_Mann_a3> <RCSB:scat_Cromer_Mann_a4>9.89330</RCSB:scat_Cromer_Mann_a4> <RCSB:scat_Cromer_Mann_b1>2.01250</RCSB:scat_Cromer_Mann_b1> <RCSB:scat_Cromer_Mann_b2>28.9975</RCSB:scat_Cromer_Mann_b2> <RCSB:scat_Cromer_Mann_b3>1.16630</RCSB:scat_Cromer_Mann_b3> <RCSB:scat_Cromer_Mann_b4>0.582600</RCSB:scat_Cromer_Mann_b4> <RCSB:scat_Cromer_Mann_c>-11.529</RCSB:scat_Cromer_Mann_c> </RCSB:atom_type> <RCSB:atom_type symbol="O"> <RCSB:oxidation_number>0</RCSB:oxidation_number> <RCSB:scat_Cromer_Mann_a1>3.04850</RCSB:scat_Cromer_Mann_a1> <RCSB:scat_Cromer_Mann_a2>13.2771</RCSB:scat_Cromer_Mann_a2> <RCSB:scat_Cromer_Mann_a3>2.28680</RCSB:scat_Cromer_Mann_a3> <RCSB:scat_Cromer_Mann_a4>5.70110</RCSB:scat_Cromer_Mann_a4> <RCSB:scat_Cromer_Mann_b1>1.54630</RCSB:scat_Cromer_Mann_b1> <RCSB:scat_Cromer_Mann_b2>0.323900</RCSB:scat_Cromer_Mann_b2> <RCSB:scat_Cromer_Mann_b3>0.867000</RCSB:scat_Cromer_Mann_b3> <RCSB:scat_Cromer_Mann_b4>32.9089</RCSB:scat_Cromer_Mann_b4> <RCSB:scat_Cromer_Mann_c>0.250800</RCSB:scat_Cromer_Mann_c> </RCSB:atom_type> <RCSB:atom_type symbol="S"> <RCSB:oxidation_number>0</RCSB:oxidation_number> <RCSB:scat_Cromer_Mann_a1>6.90530</RCSB:scat_Cromer_Mann_a1> <RCSB:scat_Cromer_Mann_a2>1.46790</RCSB:scat_Cromer_Mann_a2> <RCSB:scat_Cromer_Mann_a3>5.20340</RCSB:scat_Cromer_Mann_a3> <RCSB:scat_Cromer_Mann_a4>22.2151</RCSB:scat_Cromer_Mann_a4> <RCSB:scat_Cromer_Mann_b1>1.43790</RCSB:scat_Cromer_Mann_b1> <RCSB:scat_Cromer_Mann_b2>0.253600</RCSB:scat_Cromer_Mann_b2> <RCSB:scat_Cromer_Mann_b3>1.58630</RCSB:scat_Cromer_Mann_b3> <RCSB:scat_Cromer_Mann_b4>56.1720</RCSB:scat_Cromer_Mann_b4> <RCSB:scat_Cromer_Mann_c>0.866900</RCSB:scat_Cromer_Mann_c> </RCSB:atom_type> <RCSB:atom_type symbol="CL"> <RCSB:oxidation_number>-1</RCSB:oxidation_number> <RCSB:scat_Cromer_Mann_a1>18.2915</RCSB:scat_Cromer_Mann_a1> <RCSB:scat_Cromer_Mann_a2>0.006600</RCSB:scat_Cromer_Mann_a2> <RCSB:scat_Cromer_Mann_a3>7.20840</RCSB:scat_Cromer_Mann_a3> <RCSB:scat_Cromer_Mann_a4>1.17170</RCSB:scat_Cromer_Mann_a4> <RCSB:scat_Cromer_Mann_b1>6.53370</RCSB:scat_Cromer_Mann_b1> <RCSB:scat_Cromer_Mann_b2>19.5424</RCSB:scat_Cromer_Mann_b2> <RCSB:scat_Cromer_Mann_b3>2.33860</RCSB:scat_Cromer_Mann_b3> <RCSB:scat_Cromer_Mann_b4>60.4486</RCSB:scat_Cromer_Mann_b4> <RCSB:scat_Cromer_Mann_c>-16.378</RCSB:scat_Cromer_Mann_c> </RCSB:atom_type> </RCSB:atom_typeCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. <RCSB:atom_typeCategory> <RCSB:atom_type symbol="C"> <RCSB:oxidation_number>0</RCSB:oxidation_number> <RCSB:number_in_cell>72</RCSB:number_in_cell> <RCSB:scat_dispersion_real>.017</RCSB:scat_dispersion_real> <RCSB:scat_dispersion_imag>.009</RCSB:scat_dispersion_imag> <RCSB:scat_source>International_Tables_Vol_IV_Table_2.2B</RCSB:scat_source> </RCSB:atom_type> <RCSB:atom_type symbol="H"> <RCSB:oxidation_number>0</RCSB:oxidation_number> <RCSB:number_in_cell>100</RCSB:number_in_cell> <RCSB:scat_dispersion_real>0.</RCSB:scat_dispersion_real> <RCSB:scat_dispersion_imag>0.</RCSB:scat_dispersion_imag> <RCSB:scat_source>International_Tables_Vol_IV_Table_2.2B</RCSB:scat_source> </RCSB:atom_type> <RCSB:atom_type symbol="O"> <RCSB:oxidation_number>0</RCSB:oxidation_number> <RCSB:number_in_cell>12</RCSB:number_in_cell> <RCSB:scat_dispersion_real>.047</RCSB:scat_dispersion_real> <RCSB:scat_dispersion_imag>.032</RCSB:scat_dispersion_imag> <RCSB:scat_source>International_Tables_Vol_IV_Table_2.2B</RCSB:scat_source> </RCSB:atom_type> <RCSB:atom_type symbol="N"> <RCSB:oxidation_number>0</RCSB:oxidation_number> <RCSB:number_in_cell>4</RCSB:number_in_cell> <RCSB:scat_dispersion_real>.029</RCSB:scat_dispersion_real> <RCSB:scat_dispersion_imag>.018</RCSB:scat_dispersion_imag> <RCSB:scat_source>International_Tables_Vol_IV_Table_2.2B</RCSB:scat_source> </RCSB:atom_type> </RCSB: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 <RCSB:auditCategory> <RCSB:audit revision_id="1"> <RCSB:creation_date>1992-12-08</RCSB:creation_date> <RCSB:creation_method> Created by hand from PDB entry 5HVP, from the J. Biol. Chem. paper describing this structure and from laboratory records</RCSB:creation_method> <RCSB: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</RCSB:update_record> </RCSB:audit> </RCSB:auditCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. <RCSB:auditCategory> <RCSB:audit> <RCSB:creation_date>1991-03-20</RCSB:creation_date> <RCSB:creation_method>from_xtal_archive_file_using_CIFIO</RCSB:creation_method> <RCSB: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.</RCSB:update_record> </RCSB:audit> </RCSB: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 <RCSB:audit_authorCategory> <RCSB:audit_author name="Fitzgerald, Paula M.D."> <RCSB:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</RCSB:address> </RCSB:audit_author> <RCSB:audit_author name="McKeever, Brian M."> <RCSB:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</RCSB:address> </RCSB:audit_author> <RCSB:audit_author name="Van Middlesworth, J.F."> <RCSB:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</RCSB:address> </RCSB:audit_author> <RCSB:audit_author name="Springer, James P."> <RCSB:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</RCSB:address> </RCSB:audit_author> </RCSB: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. <RCSB:audit_conformCategory> <RCSB:audit_conform dict_name="cif_core.dic" dict_version="2.0"> <RCSB:dict_location>ftp://ftp.iucr.ac.uk/pub/cifdic.c96</RCSB:dict_location> </RCSB:audit_conform> </RCSB: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 <RCSB:audit_contact_authorCategory> <RCSB:audit_contact_author name="Fitzgerald, Paula M.D."> <RCSB:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</RCSB:address> <RCSB:phone>908 594 5510</RCSB:phone> <RCSB:fax>908 594 6645</RCSB:fax> <RCSB:email>paula_fitzgerald@merck.com</RCSB:email> </RCSB:audit_contact_author> </RCSB: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 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 ccp4_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 ccp4_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 ccp4_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 ccp4_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 ccp4_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 ccp4_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 ccp4_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 ccp4_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 ccp4_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 ccp4_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 ccp4_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 ccp4_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 ccp4_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 ccp4_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 ccp4_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 ccp4_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 ccp4_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 ccp4_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 ccp4_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 ccp4_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 ccp4_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 ccp4_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 ccp4_refine_tls must uniquely identify a record in the CCP4_REFINE_TLS list. Note that this item need not be a number; it can be any unique identifier. 1 A Data items in the CCP4_REFINE_TLS_GROUP category record details about a fragment of a TLS group. Properties of the TLS group are recorded in CCP4_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_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 auth_seq_id in category atom_site in the ATOM_SITE category. 1 303 5A A component of the identifier for the residue at which the TLS fragment range ends. This data item is a pointer to attribute auth_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 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 ccp4_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 ccp4_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 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 <RCSB:cellCategory> <RCSB:cell entry_id="5HVP"> <RCSB:length_a>58.39</RCSB:length_a> <RCSB:length_a_esd>0.05</RCSB:length_a_esd> <RCSB:length_b>86.70</RCSB:length_b> <RCSB:length_b_esd>0.12</RCSB:length_b_esd> <RCSB:length_c>46.27</RCSB:length_c> <RCSB:length_c_esd>0.06</RCSB:length_c_esd> <RCSB:angle_alpha>90.00</RCSB:angle_alpha> <RCSB:angle_beta>90.00</RCSB:angle_beta> <RCSB:angle_gamma>90.00</RCSB:angle_gamma> <RCSB:volume>234237.</RCSB:volume> <RCSB: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.</RCSB:details> </RCSB:cell> </RCSB:cellCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. <RCSB:cellCategory> <RCSB:cell> <RCSB:length_a>5.959</RCSB:length_a> <RCSB:length_a_esd>0.001</RCSB:length_a_esd> <RCSB:length_b>14.956</RCSB:length_b> <RCSB:length_b_esd>0.001</RCSB:length_b_esd> <RCSB:length_c>19.737</RCSB:length_c> <RCSB:length_c_esd>0.003</RCSB:length_c_esd> <RCSB:angle_alpha>90.0</RCSB:angle_alpha> <RCSB:angle_beta>90.0</RCSB:angle_beta> <RCSB:angle_gamma>90.0</RCSB:angle_gamma> <RCSB:volume>1759.0</RCSB:volume> <RCSB:volume_esd>0.3</RCSB:volume_esd> </RCSB:cell> </RCSB: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 <RCSB:cell_measurementCategory> <RCSB:cell_measurement entry_id="5HVP"> <RCSB:temp>293.</RCSB:temp> <RCSB:temp_esd>3.</RCSB:temp_esd> <RCSB:theta_min>11.</RCSB:theta_min> <RCSB:theta_max>31.</RCSB:theta_max> <RCSB:wavelength>1.54</RCSB:wavelength> </RCSB:cell_measurement> </RCSB:cell_measurementCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. <RCSB:cell_measurementCategory> <RCSB:cell_measurement> <RCSB:temp>293.</RCSB:temp> <RCSB:reflns_used>25</RCSB:reflns_used> <RCSB:theta_min>25.</RCSB:theta_min> <RCSB:theta_max>31.</RCSB:theta_max> </RCSB:cell_measurement> </RCSB: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). <RCSB:cell_measurement_reflnCategory> <RCSB:cell_measurement_refln index_h="-2" index_k="4" index_l="1"> <RCSB:theta>8.67</RCSB:theta> </RCSB:cell_measurement_refln> <RCSB:cell_measurement_refln index_h="0" index_k="3" index_l="2"> <RCSB:theta>9.45</RCSB:theta> </RCSB:cell_measurement_refln> <RCSB:cell_measurement_refln index_h="3" index_k="0" index_l="2"> <RCSB:theta>9.46</RCSB:theta> </RCSB:cell_measurement_refln> <RCSB:cell_measurement_refln index_h="-3" index_k="4" index_l="1"> <RCSB:theta>8.93</RCSB:theta> </RCSB:cell_measurement_refln> <RCSB:cell_measurement_refln index_h="-2" index_k="1" index_l="-2"> <RCSB:theta>7.53</RCSB:theta> </RCSB:cell_measurement_refln> <RCSB:cell_measurement_refln index_h="10" index_k="0" index_l="0"> <RCSB:theta>23.77</RCSB:theta> </RCSB:cell_measurement_refln> <RCSB:cell_measurement_refln index_h="0" index_k="10" index_l="0"> <RCSB:theta>23.78</RCSB:theta> </RCSB:cell_measurement_refln> <RCSB:cell_measurement_refln index_h="-5" index_k="4" index_l="1"> <RCSB:theta>11.14</RCSB:theta> </RCSB:cell_measurement_refln> </RCSB: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 <RCSB:chem_compCategory> <RCSB:chem_comp id="phe"> <RCSB:model_source>1987 Protin/Prolsq Ideals file</RCSB:model_source> <RCSB:name>phenylalanine</RCSB:name> </RCSB:chem_comp> <RCSB:chem_comp id="val"> <RCSB:model_source>1987 Protin/Prolsq Ideals file</RCSB:model_source> <RCSB:name>alanine</RCSB:name> </RCSB:chem_comp> </RCSB: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 A type classification of this chemical component. A serial number used by PDB in the FORMUL record. 3 Formal charge for component. A synonym for the name of the component. ATP A type classification of this chemical component. Older NDB internal type code. 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 A preliminary classification used by PDB to indicate that the chemistry of this component while described as clearly as possible is still ambiguous. Software tools may not be able to process this component definition. Identifies the attribute id in category chem_comp of the component that has replaced this component. q11 tvx Identifies the attribute id's in category chem_comp of the components which have been replaced by this component. Multiple id codes should be separated by commas. q11 tvx,atv Chemical Abstract Service identifier. Internal classifier used to organize ligand dictionary (broad chemical class). HETEROCYCLIC AROMATIC COMPOUNDS Internal classifier used to organize ligand dictionary (notable chemical features). COMPOUNDS WITH THIAZOLIDINE Date component was added to database. For nonstandard components a text description of modification of the parent component. ATP Date component was last modified. NSC identifier for component. Previous chemical name used for this component if a name correction has been made. SMILES code for component. Release status of component Modification flag. 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 <RCSB:chem_comp_angleCategory> <RCSB:chem_comp_angle comp_id="phe" atom_id_1="N" atom_id_2="CA" atom_id_3="C"> <RCSB:value_angle>xxx.xx</RCSB:value_angle> <RCSB:value_dist>x.xx</RCSB:value_dist> </RCSB:chem_comp_angle> <RCSB:chem_comp_angle comp_id="phe" atom_id_1="CA" atom_id_2="C" atom_id_3="O"> <RCSB:value_angle>xxx.xx</RCSB:value_angle> <RCSB:value_dist>x.xx</RCSB:value_dist> </RCSB:chem_comp_angle> <RCSB:chem_comp_angle comp_id="phe" atom_id_1="CB" atom_id_2="CA" atom_id_3="C"> <RCSB:value_angle>xxx.xx</RCSB:value_angle> <RCSB:value_dist>x.xx</RCSB:value_dist> </RCSB:chem_comp_angle> <RCSB:chem_comp_angle comp_id="phe" atom_id_1="CB" atom_id_2="CA" atom_id_3="N"> <RCSB:value_angle>xxx.xx</RCSB:value_angle> <RCSB:value_dist>x.xx</RCSB:value_dist> </RCSB:chem_comp_angle> <RCSB:chem_comp_angle comp_id="phe" atom_id_1="CA" atom_id_2="CB" atom_id_3="CG"> <RCSB:value_angle>xxx.xx</RCSB:value_angle> <RCSB:value_dist>x.xx</RCSB:value_dist> </RCSB:chem_comp_angle> <RCSB:chem_comp_angle comp_id="phe" atom_id_1="CB" atom_id_2="CG" atom_id_3="CD1"> <RCSB:value_angle>xxx.xx</RCSB:value_angle> <RCSB:value_dist>x.xx</RCSB:value_dist> </RCSB:chem_comp_angle> <RCSB:chem_comp_angle comp_id="phe" atom_id_1="CB" atom_id_2="CG" atom_id_3="CD2"> <RCSB:value_angle>xxx.xx</RCSB:value_angle> <RCSB:value_dist>x.xx</RCSB:value_dist> </RCSB:chem_comp_angle> <RCSB:chem_comp_angle comp_id="phe" atom_id_1="CD1" atom_id_2="CG" atom_id_3="CD2"> <RCSB:value_angle>xxx.xx</RCSB:value_angle> <RCSB:value_dist>x.xx</RCSB:value_dist> </RCSB:chem_comp_angle> <RCSB:chem_comp_angle comp_id="phe" atom_id_1="CG" atom_id_2="CD1" atom_id_3="CE1"> <RCSB:value_angle>xxx.xx</RCSB:value_angle> <RCSB:value_dist>x.xx</RCSB:value_dist> </RCSB:chem_comp_angle> <RCSB:chem_comp_angle comp_id="phe" atom_id_1="CD1" atom_id_2="CE1" atom_id_3="CZ"> <RCSB:value_angle>xxx.xx</RCSB:value_angle> <RCSB:value_dist>x.xx</RCSB:value_dist> </RCSB:chem_comp_angle> <RCSB:chem_comp_angle comp_id="phe" atom_id_1="CE1" atom_id_2="CZ" atom_id_3="CE2"> <RCSB:value_angle>xxx.xx</RCSB:value_angle> <RCSB:value_dist>x.xx</RCSB:value_dist> </RCSB:chem_comp_angle> <RCSB:chem_comp_angle comp_id="phe" atom_id_1="CZ" atom_id_2="CE2" atom_id_3="CD2"> <RCSB:value_angle>xxx.xx</RCSB:value_angle> <RCSB:value_dist>x.xx</RCSB:value_dist> </RCSB:chem_comp_angle> <RCSB:chem_comp_angle comp_id="phe" atom_id_1="CG" atom_id_2="CD2" atom_id_3="CE2"> <RCSB:value_angle>xxx.xx</RCSB:value_angle> <RCSB:value_dist>x.xx</RCSB:value_dist> </RCSB:chem_comp_angle> <RCSB:chem_comp_angle comp_id="val" atom_id_1="N" atom_id_2="CA" atom_id_3="C"> <RCSB:value_angle>xxx.xx</RCSB:value_angle> <RCSB:value_dist>x.xx</RCSB:value_dist> </RCSB:chem_comp_angle> <RCSB:chem_comp_angle comp_id="val" atom_id_1="CA" atom_id_2="C" atom_id_3="O"> <RCSB:value_angle>xxx.xx</RCSB:value_angle> <RCSB:value_dist>x.xx</RCSB:value_dist> </RCSB:chem_comp_angle> <RCSB:chem_comp_angle comp_id="val" atom_id_1="CB" atom_id_2="CA" atom_id_3="C"> <RCSB:value_angle>xxx.xx</RCSB:value_angle> <RCSB:value_dist>x.xx</RCSB:value_dist> </RCSB:chem_comp_angle> <RCSB:chem_comp_angle comp_id="val" atom_id_1="CB" atom_id_2="CA" atom_id_3="N"> <RCSB:value_angle>xxx.xx</RCSB:value_angle> <RCSB:value_dist>x.xx</RCSB:value_dist> </RCSB:chem_comp_angle> <RCSB:chem_comp_angle comp_id="val" atom_id_1="CA" atom_id_2="CB" atom_id_3="CG1"> <RCSB:value_angle>xxx.xx</RCSB:value_angle> <RCSB:value_dist>x.xx</RCSB:value_dist> </RCSB:chem_comp_angle> <RCSB:chem_comp_angle comp_id="val" atom_id_1="CA" atom_id_2="CB" atom_id_3="CG2"> <RCSB:value_angle>xxx.xx</RCSB:value_angle> <RCSB:value_dist>x.xx</RCSB:value_dist> </RCSB:chem_comp_angle> <RCSB:chem_comp_angle comp_id="val" atom_id_1="CG1" atom_id_2="CB" atom_id_3="CG2"> <RCSB:value_angle>xxx.xx</RCSB:value_angle> <RCSB:value_dist>x.xx</RCSB:value_dist> </RCSB:chem_comp_angle> </RCSB: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 <RCSB:chem_comp_atomCategory> <RCSB:chem_comp_atom comp_id="phe" atom_id="N"> <RCSB:type_symbol>N</RCSB:type_symbol> <RCSB:substruct_code>main</RCSB:substruct_code> <RCSB:model_Cartn_x>1.20134</RCSB:model_Cartn_x> <RCSB:model_Cartn_y>0.84658</RCSB:model_Cartn_y> <RCSB:model_Cartn_z>0.00000</RCSB:model_Cartn_z> </RCSB:chem_comp_atom> <RCSB:chem_comp_atom comp_id="phe" atom_id="CA"> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:substruct_code>main</RCSB:substruct_code> <RCSB:model_Cartn_x>0.00000</RCSB:model_Cartn_x> <RCSB:model_Cartn_y>0.00000</RCSB:model_Cartn_y> <RCSB:model_Cartn_z>0.00000</RCSB:model_Cartn_z> </RCSB:chem_comp_atom> <RCSB:chem_comp_atom comp_id="phe" atom_id="C"> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:substruct_code>main</RCSB:substruct_code> <RCSB:model_Cartn_x>-1.25029</RCSB:model_Cartn_x> <RCSB:model_Cartn_y>0.88107</RCSB:model_Cartn_y> <RCSB:model_Cartn_z>0.00000</RCSB:model_Cartn_z> </RCSB:chem_comp_atom> <RCSB:chem_comp_atom comp_id="phe" atom_id="O"> <RCSB:type_symbol>O</RCSB:type_symbol> <RCSB:substruct_code>main</RCSB:substruct_code> <RCSB:model_Cartn_x>-2.18525</RCSB:model_Cartn_x> <RCSB:model_Cartn_y>0.66029</RCSB:model_Cartn_y> <RCSB:model_Cartn_z>-0.78409</RCSB:model_Cartn_z> </RCSB:chem_comp_atom> <RCSB:chem_comp_atom comp_id="phe" atom_id="CB"> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:substruct_code>side</RCSB:substruct_code> <RCSB:model_Cartn_x>0.00662</RCSB:model_Cartn_x> <RCSB:model_Cartn_y>-1.03603</RCSB:model_Cartn_y> <RCSB:model_Cartn_z>1.11081</RCSB:model_Cartn_z> </RCSB:chem_comp_atom> <RCSB:chem_comp_atom comp_id="phe" atom_id="CG"> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:substruct_code>side</RCSB:substruct_code> <RCSB:model_Cartn_x>0.03254</RCSB:model_Cartn_x> <RCSB:model_Cartn_y>-0.49711</RCSB:model_Cartn_y> <RCSB:model_Cartn_z>2.50951</RCSB:model_Cartn_z> </RCSB:chem_comp_atom> <RCSB:chem_comp_atom comp_id="phe" atom_id="CD1"> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:substruct_code>side</RCSB:substruct_code> <RCSB:model_Cartn_x>-1.15813</RCSB:model_Cartn_x> <RCSB:model_Cartn_y>-0.12084</RCSB:model_Cartn_y> <RCSB:model_Cartn_z>3.13467</RCSB:model_Cartn_z> </RCSB:chem_comp_atom> <RCSB:chem_comp_atom comp_id="phe" atom_id="CE1"> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:substruct_code>side</RCSB:substruct_code> <RCSB:model_Cartn_x>-1.15720</RCSB:model_Cartn_x> <RCSB:model_Cartn_y>0.38038</RCSB:model_Cartn_y> <RCSB:model_Cartn_z>4.42732</RCSB:model_Cartn_z> </RCSB:chem_comp_atom> <RCSB:chem_comp_atom comp_id="phe" atom_id="CZ"> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:substruct_code>side</RCSB:substruct_code> <RCSB:model_Cartn_x>0.05385</RCSB:model_Cartn_x> <RCSB:model_Cartn_y>0.51332</RCSB:model_Cartn_y> <RCSB:model_Cartn_z>5.11032</RCSB:model_Cartn_z> </RCSB:chem_comp_atom> <RCSB:chem_comp_atom comp_id="phe" atom_id="CE2"> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:substruct_code>side</RCSB:substruct_code> <RCSB:model_Cartn_x>1.26137</RCSB:model_Cartn_x> <RCSB:model_Cartn_y>0.11613</RCSB:model_Cartn_y> <RCSB:model_Cartn_z>4.50975</RCSB:model_Cartn_z> </RCSB:chem_comp_atom> <RCSB:chem_comp_atom comp_id="phe" atom_id="CD2"> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:substruct_code>side</RCSB:substruct_code> <RCSB:model_Cartn_x>1.23668</RCSB:model_Cartn_x> <RCSB:model_Cartn_y>-0.38351</RCSB:model_Cartn_y> <RCSB:model_Cartn_z>3.20288</RCSB:model_Cartn_z> </RCSB:chem_comp_atom> <RCSB:chem_comp_atom comp_id="val" atom_id="N"> <RCSB:type_symbol>N</RCSB:type_symbol> <RCSB:substruct_code>main</RCSB:substruct_code> <RCSB:model_Cartn_x>1.20134</RCSB:model_Cartn_x> <RCSB:model_Cartn_y>0.84658</RCSB:model_Cartn_y> <RCSB:model_Cartn_z>0.00000</RCSB:model_Cartn_z> </RCSB:chem_comp_atom> <RCSB:chem_comp_atom comp_id="val" atom_id="CA"> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:substruct_code>main</RCSB:substruct_code> <RCSB:model_Cartn_x>0.00000</RCSB:model_Cartn_x> <RCSB:model_Cartn_y>0.00000</RCSB:model_Cartn_y> <RCSB:model_Cartn_z>0.00000</RCSB:model_Cartn_z> </RCSB:chem_comp_atom> <RCSB:chem_comp_atom comp_id="val" atom_id="C"> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:substruct_code>main</RCSB:substruct_code> <RCSB:model_Cartn_x>-1.25029</RCSB:model_Cartn_x> <RCSB:model_Cartn_y>0.88107</RCSB:model_Cartn_y> <RCSB:model_Cartn_z>0.00000</RCSB:model_Cartn_z> </RCSB:chem_comp_atom> <RCSB:chem_comp_atom comp_id="val" atom_id="O"> <RCSB:type_symbol>O</RCSB:type_symbol> <RCSB:substruct_code>main</RCSB:substruct_code> <RCSB:model_Cartn_x>-2.18525</RCSB:model_Cartn_x> <RCSB:model_Cartn_y>0.66029</RCSB:model_Cartn_y> <RCSB:model_Cartn_z>-0.78409</RCSB:model_Cartn_z> </RCSB:chem_comp_atom> <RCSB:chem_comp_atom comp_id="val" atom_id="CB"> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:substruct_code>side</RCSB:substruct_code> <RCSB:model_Cartn_x>0.05260</RCSB:model_Cartn_x> <RCSB:model_Cartn_y>-0.99339</RCSB:model_Cartn_y> <RCSB:model_Cartn_z>1.17429</RCSB:model_Cartn_z> </RCSB:chem_comp_atom> <RCSB:chem_comp_atom comp_id="val" atom_id="CG1"> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:substruct_code>side</RCSB:substruct_code> <RCSB:model_Cartn_x>-0.13288</RCSB:model_Cartn_x> <RCSB:model_Cartn_y>-0.31545</RCSB:model_Cartn_y> <RCSB:model_Cartn_z>2.52668</RCSB:model_Cartn_z> </RCSB:chem_comp_atom> <RCSB:chem_comp_atom comp_id="val" atom_id="CG2"> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:substruct_code>side</RCSB:substruct_code> <RCSB:model_Cartn_x>-0.94265</RCSB:model_Cartn_x> <RCSB:model_Cartn_y>-2.12930</RCSB:model_Cartn_y> <RCSB:model_Cartn_z>0.99811</RCSB:model_Cartn_z> </RCSB:chem_comp_atom> </RCSB: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. Ordinal index for the component atom list. Atom name alignment offset in PDB atom field. 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 <RCSB:chem_comp_bondCategory> <RCSB:chem_comp_bond comp_id="phe" atom_id_1="N" atom_id_2="CA"> <RCSB:value_order>sing</RCSB:value_order> <RCSB:value_dist>x.xx</RCSB:value_dist> </RCSB:chem_comp_bond> <RCSB:chem_comp_bond comp_id="phe" atom_id_1="CA" atom_id_2="C"> <RCSB:value_order>sing</RCSB:value_order> <RCSB:value_dist>x.xx</RCSB:value_dist> </RCSB:chem_comp_bond> <RCSB:chem_comp_bond comp_id="phe" atom_id_1="C" atom_id_2="O"> <RCSB:value_order>doub</RCSB:value_order> <RCSB:value_dist>x.xx</RCSB:value_dist> </RCSB:chem_comp_bond> <RCSB:chem_comp_bond comp_id="phe" atom_id_1="CB" atom_id_2="CA"> <RCSB:value_order>sing</RCSB:value_order> <RCSB:value_dist>x.xx</RCSB:value_dist> </RCSB:chem_comp_bond> <RCSB:chem_comp_bond comp_id="phe" atom_id_1="CB" atom_id_2="CG"> <RCSB:value_order>sing</RCSB:value_order> <RCSB:value_dist>x.xx</RCSB:value_dist> </RCSB:chem_comp_bond> <RCSB:chem_comp_bond comp_id="phe" atom_id_1="CG" atom_id_2="CD1"> <RCSB:value_order>arom</RCSB:value_order> <RCSB:value_dist>x.xx</RCSB:value_dist> </RCSB:chem_comp_bond> <RCSB:chem_comp_bond comp_id="phe" atom_id_1="CD1" atom_id_2="CE1"> <RCSB:value_order>arom</RCSB:value_order> <RCSB:value_dist>x.xx</RCSB:value_dist> </RCSB:chem_comp_bond> <RCSB:chem_comp_bond comp_id="phe" atom_id_1="CE1" atom_id_2="CZ"> <RCSB:value_order>arom</RCSB:value_order> <RCSB:value_dist>x.xx</RCSB:value_dist> </RCSB:chem_comp_bond> <RCSB:chem_comp_bond comp_id="phe" atom_id_1="CZ" atom_id_2="CE2"> <RCSB:value_order>arom</RCSB:value_order> <RCSB:value_dist>x.xx</RCSB:value_dist> </RCSB:chem_comp_bond> <RCSB:chem_comp_bond comp_id="phe" atom_id_1="CE2" atom_id_2="CD2"> <RCSB:value_order>arom</RCSB:value_order> <RCSB:value_dist>x.xx</RCSB:value_dist> </RCSB:chem_comp_bond> <RCSB:chem_comp_bond comp_id="phe" atom_id_1="CD2" atom_id_2="CG"> <RCSB:value_order>arom</RCSB:value_order> <RCSB:value_dist>x.xx</RCSB:value_dist> </RCSB:chem_comp_bond> <RCSB:chem_comp_bond comp_id="val" atom_id_1="N" atom_id_2="CA"> <RCSB:value_order>sing</RCSB:value_order> <RCSB:value_dist>x.xx</RCSB:value_dist> </RCSB:chem_comp_bond> <RCSB:chem_comp_bond comp_id="val" atom_id_1="CA" atom_id_2="C"> <RCSB:value_order>sing</RCSB:value_order> <RCSB:value_dist>x.xx</RCSB:value_dist> </RCSB:chem_comp_bond> <RCSB:chem_comp_bond comp_id="val" atom_id_1="C" atom_id_2="O"> <RCSB:value_order>doub</RCSB:value_order> <RCSB:value_dist>x.xx</RCSB:value_dist> </RCSB:chem_comp_bond> <RCSB:chem_comp_bond comp_id="val" atom_id_1="CB" atom_id_2="CA"> <RCSB:value_order>sing</RCSB:value_order> <RCSB:value_dist>x.xx</RCSB:value_dist> </RCSB:chem_comp_bond> <RCSB:chem_comp_bond comp_id="val" atom_id_1="CB" atom_id_2="CG1"> <RCSB:value_order>sing</RCSB:value_order> <RCSB:value_dist>x.xx</RCSB:value_dist> </RCSB:chem_comp_bond> <RCSB:chem_comp_bond comp_id="val" atom_id_1="CB" atom_id_2="CG2"> <RCSB:value_order>sing</RCSB:value_order> <RCSB:value_dist>x.xx</RCSB:value_dist> </RCSB:chem_comp_bond> </RCSB:chem_comp_bondCategory> Ordinal index for the component bond list. 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 <RCSB:chem_comp_chirCategory> <RCSB:chem_comp_chir comp_id="phe" id="phe1"> <RCSB:atom_id>CA</RCSB:atom_id> </RCSB:chem_comp_chir> <RCSB:chem_comp_chir comp_id="val" id="val1"> <RCSB:atom_id>CA</RCSB:atom_id> </RCSB:chem_comp_chir> </RCSB: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 <RCSB:chem_comp_chir_atomCategory> <RCSB:chem_comp_chir_atom comp_id="phe" chir_id="1" atom_id="N"></RCSB:chem_comp_chir_atom> <RCSB:chem_comp_chir_atom comp_id="phe" chir_id="1" atom_id="C"></RCSB:chem_comp_chir_atom> <RCSB:chem_comp_chir_atom comp_id="phe" chir_id="1" atom_id="CB"></RCSB:chem_comp_chir_atom> <RCSB:chem_comp_chir_atom comp_id="val" chir_id="1" atom_id="N"></RCSB:chem_comp_chir_atom> <RCSB:chem_comp_chir_atom comp_id="val" chir_id="1" atom_id="C"></RCSB:chem_comp_chir_atom> <RCSB:chem_comp_chir_atom comp_id="val" chir_id="1" atom_id="CB"></RCSB:chem_comp_chir_atom> </RCSB: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. <RCSB:chem_comp_linkCategory> <RCSB:chem_comp_link link_id="ribose_adenine"> <RCSB:type_comp_1>ribose</RCSB:type_comp_1> <RCSB:type_comp_2>adenine</RCSB:type_comp_2> <RCSB:details> Defines the linkage between adenine base and ribose sugar</RCSB:details> </RCSB:chem_comp_link> </RCSB: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 <RCSB:chem_comp_planeCategory> <RCSB:chem_comp_plane comp_id="phe" id="phe1"></RCSB:chem_comp_plane> </RCSB: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 <RCSB:chem_comp_plane_atomCategory> <RCSB:chem_comp_plane_atom plane_id="phe1" comp_id="phe" atom_id="CB"></RCSB:chem_comp_plane_atom> <RCSB:chem_comp_plane_atom plane_id="phe1" comp_id="phe" atom_id="CG"></RCSB:chem_comp_plane_atom> <RCSB:chem_comp_plane_atom plane_id="phe1" comp_id="phe" atom_id="CD1"></RCSB:chem_comp_plane_atom> <RCSB:chem_comp_plane_atom plane_id="phe1" comp_id="phe" atom_id="CE1"></RCSB:chem_comp_plane_atom> <RCSB:chem_comp_plane_atom plane_id="phe1" comp_id="phe" atom_id="CZ"></RCSB:chem_comp_plane_atom> <RCSB:chem_comp_plane_atom plane_id="phe1" comp_id="phe" atom_id="CE2"></RCSB:chem_comp_plane_atom> <RCSB:chem_comp_plane_atom plane_id="phe1" comp_id="phe" atom_id="CD2"></RCSB:chem_comp_plane_atom> </RCSB: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 <RCSB:chem_comp_torCategory> <RCSB:chem_comp_tor comp_id="phe" id="phe_chi1"> <RCSB:atom_id_1>N</RCSB:atom_id_1> <RCSB:atom_id_2>CA</RCSB:atom_id_2> <RCSB:atom_id_3>CB</RCSB:atom_id_3> <RCSB:atom_id_4>CG</RCSB:atom_id_4> </RCSB:chem_comp_tor> <RCSB:chem_comp_tor comp_id="phe" id="phe_chi2"> <RCSB:atom_id_1>CA</RCSB:atom_id_1> <RCSB:atom_id_2>CB</RCSB:atom_id_2> <RCSB:atom_id_3>CG</RCSB:atom_id_3> <RCSB:atom_id_4>CD1</RCSB:atom_id_4> </RCSB:chem_comp_tor> <RCSB:chem_comp_tor comp_id="phe" id="phe_ring1"> <RCSB:atom_id_1>CB</RCSB:atom_id_1> <RCSB:atom_id_2>CG</RCSB:atom_id_2> <RCSB:atom_id_3>CD1</RCSB:atom_id_3> <RCSB:atom_id_4>CE1</RCSB:atom_id_4> </RCSB:chem_comp_tor> <RCSB:chem_comp_tor comp_id="phe" id="phe_ring2"> <RCSB:atom_id_1>CB</RCSB:atom_id_1> <RCSB:atom_id_2>CG</RCSB:atom_id_2> <RCSB:atom_id_3>CD2</RCSB:atom_id_3> <RCSB:atom_id_4>CE2</RCSB:atom_id_4> </RCSB:chem_comp_tor> <RCSB:chem_comp_tor comp_id="phe" id="phe_ring3"> <RCSB:atom_id_1>CG</RCSB:atom_id_1> <RCSB:atom_id_2>CD1</RCSB:atom_id_2> <RCSB:atom_id_3>CE1</RCSB:atom_id_3> <RCSB:atom_id_4>CZ</RCSB:atom_id_4> </RCSB:chem_comp_tor> <RCSB:chem_comp_tor comp_id="phe" id="phe_ring4"> <RCSB:atom_id_1>CD1</RCSB:atom_id_1> <RCSB:atom_id_2>CE1</RCSB:atom_id_2> <RCSB:atom_id_3>CZ</RCSB:atom_id_3> <RCSB:atom_id_4>CE2</RCSB:atom_id_4> </RCSB:chem_comp_tor> <RCSB:chem_comp_tor comp_id="phe" id="phe_ring5"> <RCSB:atom_id_1>CE1</RCSB:atom_id_1> <RCSB:atom_id_2>CZ</RCSB:atom_id_2> <RCSB:atom_id_3>CE2</RCSB:atom_id_3> <RCSB:atom_id_4>CD2</RCSB:atom_id_4> </RCSB:chem_comp_tor> </RCSB: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 <RCSB:chem_comp_tor_valueCategory> <RCSB:chem_comp_tor_value tor_id="phe_chi1" comp_id="phe"> <RCSB:angle>-60.0</RCSB:angle> <RCSB:dist>2.88</RCSB:dist> </RCSB:chem_comp_tor_value> <RCSB:chem_comp_tor_value tor_id="phe_chi1" comp_id="phe"> <RCSB:angle>180.0</RCSB:angle> <RCSB:dist>3.72</RCSB:dist> </RCSB:chem_comp_tor_value> <RCSB:chem_comp_tor_value tor_id="phe_chi1" comp_id="phe"> <RCSB:angle>60.0</RCSB:angle> <RCSB:dist>2.88</RCSB:dist> </RCSB:chem_comp_tor_value> <RCSB:chem_comp_tor_value tor_id="phe_chi2" comp_id="phe"> <RCSB:angle>90.0</RCSB:angle> <RCSB:dist>3.34</RCSB:dist> </RCSB:chem_comp_tor_value> <RCSB:chem_comp_tor_value tor_id="phe_chi2" comp_id="phe"> <RCSB:angle>-90.0</RCSB:angle> <RCSB:dist>3.34</RCSB:dist> </RCSB:chem_comp_tor_value> <RCSB:chem_comp_tor_value tor_id="phe_ring1" comp_id="phe"> <RCSB:angle>180.0</RCSB:angle> <RCSB:dist>3.75</RCSB:dist> </RCSB:chem_comp_tor_value> <RCSB:chem_comp_tor_value tor_id="phe_ring2" comp_id="phe"> <RCSB:angle>180.0</RCSB:angle> <RCSB:dist>3.75</RCSB:dist> </RCSB:chem_comp_tor_value> <RCSB:chem_comp_tor_value tor_id="phe_ring3" comp_id="phe"> <RCSB:angle>0.0</RCSB:angle> <RCSB:dist>2.80</RCSB:dist> </RCSB:chem_comp_tor_value> <RCSB:chem_comp_tor_value tor_id="phe_ring4" comp_id="phe"> <RCSB:angle>0.0</RCSB:angle> <RCSB:dist>2.80</RCSB:dist> </RCSB:chem_comp_tor_value> <RCSB:chem_comp_tor_value tor_id="phe_ring5" comp_id="phe"> <RCSB:angle>0.0</RCSB:angle> <RCSB:dist>2.80</RCSB:dist> </RCSB:chem_comp_tor_value> </RCSB: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 <RCSB:chem_link_angleCategory> <RCSB:chem_link_angle link_id="PEPTIDE" atom_id_1="N" atom_id_2="CA" atom_id_3="C"> <RCSB:value_angle>111.2</RCSB:value_angle> <RCSB:value_angle_esd>2.8</RCSB:value_angle_esd> <RCSB:atom_1_comp_id>1</RCSB:atom_1_comp_id> <RCSB:atom_2_comp_id>1</RCSB:atom_2_comp_id> <RCSB:atom_3_comp_id>1</RCSB:atom_3_comp_id> </RCSB:chem_link_angle> <RCSB:chem_link_angle link_id="PEPTIDE" atom_id_1="CA" atom_id_2="C" atom_id_3="O"> <RCSB:value_angle>120.8</RCSB:value_angle> <RCSB:value_angle_esd>1.7</RCSB:value_angle_esd> <RCSB:atom_1_comp_id>1</RCSB:atom_1_comp_id> <RCSB:atom_2_comp_id>1</RCSB:atom_2_comp_id> <RCSB:atom_3_comp_id>1</RCSB:atom_3_comp_id> </RCSB:chem_link_angle> <RCSB:chem_link_angle link_id="PEPTIDE" atom_id_1="CA" atom_id_2="C" atom_id_3="N"> <RCSB:value_angle>116.2</RCSB:value_angle> <RCSB:value_angle_esd>2.0</RCSB:value_angle_esd> <RCSB:atom_1_comp_id>1</RCSB:atom_1_comp_id> <RCSB:atom_2_comp_id>1</RCSB:atom_2_comp_id> <RCSB:atom_3_comp_id>2</RCSB:atom_3_comp_id> </RCSB:chem_link_angle> <RCSB:chem_link_angle link_id="PEPTIDE" atom_id_1="O" atom_id_2="C" atom_id_3="N"> <RCSB:value_angle>123.0</RCSB:value_angle> <RCSB:value_angle_esd>1.6</RCSB:value_angle_esd> <RCSB:atom_1_comp_id>1</RCSB:atom_1_comp_id> <RCSB:atom_2_comp_id>1</RCSB:atom_2_comp_id> <RCSB:atom_3_comp_id>2</RCSB:atom_3_comp_id> </RCSB:chem_link_angle> <RCSB:chem_link_angle link_id="PEPTIDE" atom_id_1="C" atom_id_2="N" atom_id_3="CA"> <RCSB:value_angle>121.7</RCSB:value_angle> <RCSB:value_angle_esd>1.8</RCSB:value_angle_esd> <RCSB:atom_1_comp_id>1</RCSB:atom_1_comp_id> <RCSB:atom_2_comp_id>2</RCSB:atom_2_comp_id> <RCSB:atom_3_comp_id>2</RCSB:atom_3_comp_id> </RCSB:chem_link_angle> </RCSB: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 <RCSB:chem_link_bondCategory> <RCSB:chem_link_bond link_id="PEPTIDE" atom_id_1="N" atom_id_2="CA"> <RCSB:value_dist>1.458</RCSB:value_dist> <RCSB:value_dist_esd>0.019</RCSB:value_dist_esd> <RCSB:atom_1_comp_id>1</RCSB:atom_1_comp_id> <RCSB:atom_2_comp_id>1</RCSB:atom_2_comp_id> </RCSB:chem_link_bond> <RCSB:chem_link_bond link_id="PEPTIDE" atom_id_1="CA" atom_id_2="C"> <RCSB:value_dist>1.525</RCSB:value_dist> <RCSB:value_dist_esd>0.021</RCSB:value_dist_esd> <RCSB:atom_1_comp_id>1</RCSB:atom_1_comp_id> <RCSB:atom_2_comp_id>1</RCSB:atom_2_comp_id> </RCSB:chem_link_bond> <RCSB:chem_link_bond link_id="PEPTIDE" atom_id_1="C" atom_id_2="N"> <RCSB:value_dist>1.329</RCSB:value_dist> <RCSB:value_dist_esd>0.014</RCSB:value_dist_esd> <RCSB:atom_1_comp_id>1</RCSB:atom_1_comp_id> <RCSB:atom_2_comp_id>2</RCSB:atom_2_comp_id> </RCSB:chem_link_bond> <RCSB:chem_link_bond link_id="PEPTIDE" atom_id_1="C" atom_id_2="O"> <RCSB:value_dist>1.231</RCSB:value_dist> <RCSB:value_dist_esd>0.020</RCSB:value_dist_esd> <RCSB:atom_1_comp_id>1</RCSB:atom_1_comp_id> <RCSB:atom_2_comp_id>1</RCSB:atom_2_comp_id> </RCSB:chem_link_bond> </RCSB: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]. <RCSB:chemicalCategory> <RCSB:chemical entry_id="9597gaus"> <RCSB:name_systematic>trans-bis(tricyclohexylphosphine)tetracarbonylmolybdenum(0)</RCSB:name_systematic> </RCSB:chemical> </RCSB: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]. <RCSB:chemical_conn_atomCategory> <RCSB:chemical_conn_atom number="1"> <RCSB:type_symbol>S</RCSB:type_symbol> <RCSB:display_x>.39</RCSB:display_x> <RCSB:display_y>.81</RCSB:display_y> <RCSB:NCA>1</RCSB:NCA> <RCSB:NH>0</RCSB:NH> </RCSB:chemical_conn_atom> <RCSB:chemical_conn_atom number="2"> <RCSB:type_symbol>S</RCSB:type_symbol> <RCSB:display_x>.39</RCSB:display_x> <RCSB:display_y>.96</RCSB:display_y> <RCSB:NCA>2</RCSB:NCA> <RCSB:NH>0</RCSB:NH> </RCSB:chemical_conn_atom> <RCSB:chemical_conn_atom number="3"> <RCSB:type_symbol>N</RCSB:type_symbol> <RCSB:display_x>.14</RCSB:display_x> <RCSB:display_y>.88</RCSB:display_y> <RCSB:NCA>3</RCSB:NCA> <RCSB:NH>0</RCSB:NH> </RCSB:chemical_conn_atom> <RCSB:chemical_conn_atom number="4"> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:display_x>.33</RCSB:display_x> <RCSB:display_y>.88</RCSB:display_y> <RCSB:NCA>3</RCSB:NCA> <RCSB:NH>0</RCSB:NH> </RCSB:chemical_conn_atom> <RCSB:chemical_conn_atom number="5"> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:display_x>.11</RCSB:display_x> <RCSB:display_y>.96</RCSB:display_y> <RCSB:NCA>2</RCSB:NCA> <RCSB:NH>2</RCSB:NH> </RCSB:chemical_conn_atom> <RCSB:chemical_conn_atom number="6"> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:display_x>.03</RCSB:display_x> <RCSB:display_y>.96</RCSB:display_y> <RCSB:NCA>2</RCSB:NCA> <RCSB:NH>2</RCSB:NH> </RCSB:chemical_conn_atom> <RCSB:chemical_conn_atom number="7"> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:display_x>.03</RCSB:display_x> <RCSB:display_y>.80</RCSB:display_y> <RCSB:NCA>2</RCSB:NCA> <RCSB:NH>2</RCSB:NH> </RCSB:chemical_conn_atom> <RCSB:chemical_conn_atom number="8"> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:display_x>.11</RCSB:display_x> <RCSB:display_y>.80</RCSB:display_y> <RCSB:NCA>2</RCSB:NCA> <RCSB:NH>2</RCSB:NH> </RCSB:chemical_conn_atom> <RCSB:chemical_conn_atom number="9"> <RCSB:type_symbol>S</RCSB:type_symbol> <RCSB:display_x>.54</RCSB:display_x> <RCSB:display_y>.81</RCSB:display_y> <RCSB:NCA>1</RCSB:NCA> <RCSB:NH>0</RCSB:NH> </RCSB:chemical_conn_atom> <RCSB:chemical_conn_atom number="10"> <RCSB:type_symbol>S</RCSB:type_symbol> <RCSB:display_x>.54</RCSB:display_x> <RCSB:display_y>.96</RCSB:display_y> <RCSB:NCA>2</RCSB:NCA> <RCSB:NH>0</RCSB:NH> </RCSB:chemical_conn_atom> <RCSB:chemical_conn_atom number="11"> <RCSB:type_symbol>N</RCSB:type_symbol> <RCSB:display_x>.80</RCSB:display_x> <RCSB:display_y>.88</RCSB:display_y> <RCSB:NCA>3</RCSB:NCA> <RCSB:NH>0</RCSB:NH> </RCSB:chemical_conn_atom> <RCSB:chemical_conn_atom number="12"> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:display_x>.60</RCSB:display_x> <RCSB:display_y>.88</RCSB:display_y> <RCSB:NCA>3</RCSB:NCA> <RCSB:NH>0</RCSB:NH> </RCSB:chemical_conn_atom> <RCSB:chemical_conn_atom number="13"> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:display_x>.84</RCSB:display_x> <RCSB:display_y>.96</RCSB:display_y> <RCSB:NCA>2</RCSB:NCA> <RCSB:NH>2</RCSB:NH> </RCSB:chemical_conn_atom> <RCSB:chemical_conn_atom number="14"> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:display_x>.91</RCSB:display_x> <RCSB:display_y>.96</RCSB:display_y> <RCSB:NCA>2</RCSB:NCA> <RCSB:NH>2</RCSB:NH> </RCSB:chemical_conn_atom> <RCSB:chemical_conn_atom number="15"> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:display_x>.91</RCSB:display_x> <RCSB:display_y>.80</RCSB:display_y> <RCSB:NCA>2</RCSB:NCA> <RCSB:NH>2</RCSB:NH> </RCSB:chemical_conn_atom> <RCSB:chemical_conn_atom number="16"> <RCSB:type_symbol>C</RCSB:type_symbol> <RCSB:display_x>.84</RCSB:display_x> <RCSB:display_y>.80</RCSB:display_y> <RCSB:NCA>2</RCSB:NCA> <RCSB:NH>2</RCSB:NH> </RCSB:chemical_conn_atom> </RCSB: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]. <RCSB:chemical_conn_bondCategory> <RCSB:chemical_conn_bond atom_1="4" atom_2="1"> <RCSB:type>doub</RCSB:type> </RCSB:chemical_conn_bond> <RCSB:chemical_conn_bond atom_1="4" atom_2="3"> <RCSB:type>sing</RCSB:type> </RCSB:chemical_conn_bond> <RCSB:chemical_conn_bond atom_1="4" atom_2="2"> <RCSB:type>sing</RCSB:type> </RCSB:chemical_conn_bond> <RCSB:chemical_conn_bond atom_1="5" atom_2="3"> <RCSB:type>sing</RCSB:type> </RCSB:chemical_conn_bond> <RCSB:chemical_conn_bond atom_1="6" atom_2="5"> <RCSB:type>sing</RCSB:type> </RCSB:chemical_conn_bond> <RCSB:chemical_conn_bond atom_1="7" atom_2="6"> <RCSB:type>sing</RCSB:type> </RCSB:chemical_conn_bond> <RCSB:chemical_conn_bond atom_1="8" atom_2="7"> <RCSB:type>sing</RCSB:type> </RCSB:chemical_conn_bond> <RCSB:chemical_conn_bond atom_1="8" atom_2="3"> <RCSB:type>sing</RCSB:type> </RCSB:chemical_conn_bond> <RCSB:chemical_conn_bond atom_1="10" atom_2="2"> <RCSB:type>sing</RCSB:type> </RCSB:chemical_conn_bond> <RCSB:chemical_conn_bond atom_1="12" atom_2="9"> <RCSB:type>doub</RCSB:type> </RCSB:chemical_conn_bond> <RCSB:chemical_conn_bond atom_1="12" atom_2="11"> <RCSB:type>sing</RCSB:type> </RCSB:chemical_conn_bond> <RCSB:chemical_conn_bond atom_1="12" atom_2="10"> <RCSB:type>sing</RCSB:type> </RCSB:chemical_conn_bond> <RCSB:chemical_conn_bond atom_1="13" atom_2="11"> <RCSB:type>sing</RCSB:type> </RCSB:chemical_conn_bond> <RCSB:chemical_conn_bond atom_1="14" atom_2="13"> <RCSB:type>sing</RCSB:type> </RCSB:chemical_conn_bond> <RCSB:chemical_conn_bond atom_1="15" atom_2="14"> <RCSB:type>sing</RCSB:type> </RCSB:chemical_conn_bond> <RCSB:chemical_conn_bond atom_1="16" atom_2="15"> <RCSB:type>sing</RCSB:type> </RCSB:chemical_conn_bond> <RCSB:chemical_conn_bond atom_1="16" atom_2="11"> <RCSB:type>sing</RCSB:type> </RCSB:chemical_conn_bond> <RCSB:chemical_conn_bond atom_1="17" atom_2="5"> <RCSB:type>sing</RCSB:type> </RCSB:chemical_conn_bond> <RCSB:chemical_conn_bond atom_1="18" atom_2="5"> <RCSB:type>sing</RCSB:type> </RCSB:chemical_conn_bond> <RCSB:chemical_conn_bond atom_1="19" atom_2="6"> <RCSB:type>sing</RCSB:type> </RCSB:chemical_conn_bond> <RCSB:chemical_conn_bond atom_1="20" atom_2="6"> <RCSB:type>sing</RCSB:type> </RCSB:chemical_conn_bond> <RCSB:chemical_conn_bond atom_1="21" atom_2="7"> <RCSB:type>sing</RCSB:type> </RCSB:chemical_conn_bond> <RCSB:chemical_conn_bond atom_1="22" atom_2="7"> <RCSB:type>sing</RCSB:type> </RCSB:chemical_conn_bond> <RCSB:chemical_conn_bond atom_1="23" atom_2="8"> <RCSB:type>sing</RCSB:type> </RCSB:chemical_conn_bond> <RCSB:chemical_conn_bond atom_1="24" atom_2="8"> <RCSB:type>sing</RCSB:type> </RCSB:chemical_conn_bond> <RCSB:chemical_conn_bond atom_1="25" atom_2="13"> <RCSB:type>sing</RCSB:type> </RCSB:chemical_conn_bond> <RCSB:chemical_conn_bond atom_1="26" atom_2="13"> <RCSB:type>sing</RCSB:type> </RCSB:chemical_conn_bond> <RCSB:chemical_conn_bond atom_1="27" atom_2="14"> <RCSB:type>sing</RCSB:type> </RCSB:chemical_conn_bond> <RCSB:chemical_conn_bond atom_1="28" atom_2="14"> <RCSB:type>sing</RCSB:type> </RCSB:chemical_conn_bond> <RCSB:chemical_conn_bond atom_1="29" atom_2="15"> <RCSB:type>sing</RCSB:type> </RCSB:chemical_conn_bond> <RCSB:chemical_conn_bond atom_1="30" atom_2="15"> <RCSB:type>sing</RCSB:type> </RCSB:chemical_conn_bond> <RCSB:chemical_conn_bond atom_1="31" atom_2="16"> <RCSB:type>sing</RCSB:type> </RCSB:chemical_conn_bond> <RCSB:chemical_conn_bond atom_1="32" atom_2="16"> <RCSB:type>sing</RCSB:type> </RCSB:chemical_conn_bond> </RCSB: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]. <RCSB:chemical_formulaCategory> <RCSB:chemical_formula entry_id="TOZ"> <RCSB:moiety>C18 H25 N O3</RCSB:moiety> <RCSB:sum>C18 H25 N O3</RCSB:sum> <RCSB:weight>303.40</RCSB:weight> </RCSB:chemical_formula> </RCSB: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 <RCSB:citationCategory> <RCSB:citation id="primary"> <RCSB:coordinate_linkage>yes</RCSB:coordinate_linkage> <RCSB:title> Crystallographic analysis of a complex between human immunodeficiency virus type 1 protease and acetyl-pepstatin at 2.0-Angstroms resolution.</RCSB:title> <RCSB:country>US</RCSB:country> <RCSB:journal_abbrev>J. Biol. Chem.</RCSB:journal_abbrev> <RCSB:journal_volume>265</RCSB:journal_volume> <RCSB:page_first>14209</RCSB:page_first> <RCSB:page_last>14219</RCSB:page_last> <RCSB:year>1990</RCSB:year> <RCSB:journal_id_ASTM>HBCHA3</RCSB:journal_id_ASTM> <RCSB:journal_id_ISSN>0021-9258</RCSB:journal_id_ISSN> <RCSB:journal_id_CSD>071</RCSB:journal_id_CSD> <RCSB:details> The publication that directly relates to this coordinate set.</RCSB:details> </RCSB:citation> <RCSB:citation id="2"> <RCSB:coordinate_linkage>no</RCSB:coordinate_linkage> <RCSB:title> Three-dimensional structure of aspartyl-protease from human immunodeficiency virus HIV-1.</RCSB:title> <RCSB:country>UK</RCSB:country> <RCSB:journal_abbrev>Nature</RCSB:journal_abbrev> <RCSB:journal_volume>337</RCSB:journal_volume> <RCSB:page_first>615</RCSB:page_first> <RCSB:page_last>619</RCSB:page_last> <RCSB:year>1989</RCSB:year> <RCSB:journal_id_ASTM>NATUAS</RCSB:journal_id_ASTM> <RCSB:journal_id_ISSN>0028-0836</RCSB:journal_id_ISSN> <RCSB:journal_id_CSD>006</RCSB:journal_id_CSD> <RCSB:details> Determination of the structure of the unliganded enzyme.</RCSB:details> </RCSB:citation> <RCSB:citation id="3"> <RCSB:coordinate_linkage>no</RCSB:coordinate_linkage> <RCSB:title> Crystallization of the aspartylprotease from human immunodeficiency virus, HIV-1.</RCSB:title> <RCSB:country>US</RCSB:country> <RCSB:journal_abbrev>J. Biol. Chem.</RCSB:journal_abbrev> <RCSB:journal_volume>264</RCSB:journal_volume> <RCSB:page_first>1919</RCSB:page_first> <RCSB:page_last>1921</RCSB:page_last> <RCSB:year>1989</RCSB:year> <RCSB:journal_id_ASTM>HBCHA3</RCSB:journal_id_ASTM> <RCSB:journal_id_ISSN>0021-9258</RCSB:journal_id_ISSN> <RCSB:journal_id_CSD>071</RCSB:journal_id_CSD> <RCSB:details> Crystallization of the unliganded enzyme.</RCSB:details> </RCSB:citation> <RCSB:citation id="4"> <RCSB:coordinate_linkage>no</RCSB:coordinate_linkage> <RCSB:title> Human immunodeficiency virus protease. Bacterial expression and characterization of the purified aspartic protease.</RCSB:title> <RCSB:country>US</RCSB:country> <RCSB:journal_abbrev>J. Biol. Chem.</RCSB:journal_abbrev> <RCSB:journal_volume>264</RCSB:journal_volume> <RCSB:page_first>2307</RCSB:page_first> <RCSB:page_last>2312</RCSB:page_last> <RCSB:year>1989</RCSB:year> <RCSB:journal_id_ASTM>HBCHA3</RCSB:journal_id_ASTM> <RCSB:journal_id_ISSN>0021-9258</RCSB:journal_id_ISSN> <RCSB:journal_id_CSD>071</RCSB:journal_id_CSD> <RCSB:details> Expression and purification of the enzyme.</RCSB:details> </RCSB:citation> </RCSB: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 List of the names of authors of the citation. Intials or first names followed by family name(s). Multiple authors separated by commas or by the word 'and'. B. H. M. Mooers, B. F. Eichman and P. S. Ho D. B. Tippin and M. Sundaralingam 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. Document Object Identifier used by doi.org to uniquely specify bibliographic entry. DOI:10.2345/S1384107697000225 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 <RCSB:citation_authorCategory> <RCSB:citation_author citation_id="primary" name="Fitzgerald, P.M.D."> <RCSB:ordinal>1</RCSB:ordinal> </RCSB:citation_author> <RCSB:citation_author citation_id="primary" name="McKeever, B.M."> <RCSB:ordinal>2</RCSB:ordinal> </RCSB:citation_author> <RCSB:citation_author citation_id="primary" name="Van Middlesworth, J.F."> <RCSB:ordinal>3</RCSB:ordinal> </RCSB:citation_author> <RCSB:citation_author citation_id="primary" name="Springer, J.P."> <RCSB:ordinal>4</RCSB:ordinal> </RCSB:citation_author> <RCSB:citation_author citation_id="primary" name="Heimbach, J.C."> <RCSB:ordinal>5</RCSB:ordinal> </RCSB:citation_author> <RCSB:citation_author citation_id="primary" name="Leu, C.-T."> <RCSB:ordinal>6</RCSB:ordinal> </RCSB:citation_author> <RCSB:citation_author citation_id="primary" name="Herber, W.K."> <RCSB:ordinal>7</RCSB:ordinal> </RCSB:citation_author> <RCSB:citation_author citation_id="primary" name="Dixon, R.A.F."> <RCSB:ordinal>8</RCSB:ordinal> </RCSB:citation_author> <RCSB:citation_author citation_id="primary" name="Darke, P.L."> <RCSB:ordinal>9</RCSB:ordinal> </RCSB:citation_author> <RCSB:citation_author citation_id="2" name="Navia, M.A."> <RCSB:ordinal>1</RCSB:ordinal> </RCSB:citation_author> <RCSB:citation_author citation_id="2" name="Fitzgerald, P.M.D."> <RCSB:ordinal>2</RCSB:ordinal> </RCSB:citation_author> <RCSB:citation_author citation_id="2" name="McKeever, B.M."> <RCSB:ordinal>3</RCSB:ordinal> </RCSB:citation_author> <RCSB:citation_author citation_id="2" name="Leu, C.-T."> <RCSB:ordinal>4</RCSB:ordinal> </RCSB:citation_author> <RCSB:citation_author citation_id="2" name="Heimbach, J.C."> <RCSB:ordinal>5</RCSB:ordinal> </RCSB:citation_author> <RCSB:citation_author citation_id="2" name="Herber, W.K."> <RCSB:ordinal>6</RCSB:ordinal> </RCSB:citation_author> <RCSB:citation_author citation_id="2" name="Sigal, I.S."> <RCSB:ordinal>7</RCSB:ordinal> </RCSB:citation_author> <RCSB:citation_author citation_id="2" name="Darke, P.L."> <RCSB:ordinal>8</RCSB:ordinal> </RCSB:citation_author> <RCSB:citation_author citation_id="2" name="Springer, J.P."> <RCSB:ordinal>9</RCSB:ordinal> </RCSB:citation_author> <RCSB:citation_author citation_id="3" name="McKeever, B.M."> <RCSB:ordinal>1</RCSB:ordinal> </RCSB:citation_author> <RCSB:citation_author citation_id="3" name="Navia, M.A."> <RCSB:ordinal>2</RCSB:ordinal> </RCSB:citation_author> <RCSB:citation_author citation_id="3" name="Fitzgerald, P.M.D."> <RCSB:ordinal>3</RCSB:ordinal> </RCSB:citation_author> <RCSB:citation_author citation_id="3" name="Springer, J.P."> <RCSB:ordinal>4</RCSB:ordinal> </RCSB:citation_author> <RCSB:citation_author citation_id="3" name="Leu, C.-T."> <RCSB:ordinal>5</RCSB:ordinal> </RCSB:citation_author> <RCSB:citation_author citation_id="3" name="Heimbach, J.C."> <RCSB:ordinal>6</RCSB:ordinal> </RCSB:citation_author> <RCSB:citation_author citation_id="3" name="Herber, W.K."> <RCSB:ordinal>7</RCSB:ordinal> </RCSB:citation_author> <RCSB:citation_author citation_id="3" name="Sigal, I.S."> <RCSB:ordinal>8</RCSB:ordinal> </RCSB:citation_author> <RCSB:citation_author citation_id="3" name="Darke, P.L."> <RCSB:ordinal>9</RCSB:ordinal> </RCSB:citation_author> <RCSB:citation_author citation_id="4" name="Darke, P.L."> <RCSB:ordinal>1</RCSB:ordinal> </RCSB:citation_author> <RCSB:citation_author citation_id="4" name="Leu, C.-T."> <RCSB:ordinal>2</RCSB:ordinal> </RCSB:citation_author> <RCSB:citation_author citation_id="4" name="Davis, L.J."> <RCSB:ordinal>3</RCSB:ordinal> </RCSB:citation_author> <RCSB:citation_author citation_id="4" name="Heimbach, J.C."> <RCSB:ordinal>4</RCSB:ordinal> </RCSB:citation_author> <RCSB:citation_author citation_id="4" name="Diehl, R.E."> <RCSB:ordinal>5</RCSB:ordinal> </RCSB:citation_author> <RCSB:citation_author citation_id="4" name="Hill, W.S."> <RCSB:ordinal>6</RCSB:ordinal> </RCSB:citation_author> <RCSB:citation_author citation_id="4" name="Dixon, R.A.F."> <RCSB:ordinal>7</RCSB:ordinal> </RCSB:citation_author> <RCSB:citation_author citation_id="4" name="Sigal, I.S."> <RCSB:ordinal>8</RCSB:ordinal> </RCSB:citation_author> </RCSB: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 <RCSB:citation_editorCategory> <RCSB:citation_editor citation_id="5" name="McKeever, B.M."></RCSB:citation_editor> <RCSB:citation_editor citation_id="5" name="Navia, M.A."></RCSB:citation_editor> <RCSB:citation_editor citation_id="5" name="Fitzgerald, P.M.D."></RCSB:citation_editor> <RCSB:citation_editor citation_id="5" name="Springer, J.P."></RCSB:citation_editor> </RCSB: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]. <RCSB:computingCategory> <RCSB:computing> <RCSB:data_collection>CAD-4 (Enraf-Nonius, 1989)</RCSB:data_collection> <RCSB:cell_refinement>CAD-4 (Enraf-Nonius, 1989)</RCSB:cell_refinement> <RCSB:data_reduction>CFEO (Solans, 1978)</RCSB:data_reduction> <RCSB:structure_solution>SHELXS86 (Sheldrick, 1990)</RCSB:structure_solution> <RCSB:structure_refinement>SHELXL93 (Sheldrick, 1993)</RCSB:structure_refinement> <RCSB:molecular_graphics>ORTEPII (Johnson, 1976)</RCSB:molecular_graphics> <RCSB:publication_material>PARST (Nardelli, 1983)</RCSB:publication_material> </RCSB:computing> </RCSB: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) Structure refinement method. Give the program or package name. Software used for generating material for publication. Give the program or package name and a brief reference. Data reduction/data scaling Give the program or package name. Data reduction/intensity integration software Give the program or package name. 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. The code assigned by the NDB. BDL001 The code assigned by the PDB. 1BNA The codes of related PDB entries. 1NK1,1NK2 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 <RCSB:database_2Category> <RCSB:database_2 database_id="PDB" database_code="5HVP"></RCSB:database_2> </RCSB: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 <RCSB:database_PDB_caveatCategory> <RCSB:database_PDB_caveat id="1"> <RCSB:text> CAVEAT 1ABC THE CRYSTAL TRANSFORMATION IS IN ERROR BUT IS</RCSB:text> </RCSB:database_PDB_caveat> <RCSB:database_PDB_caveat id="2"> <RCSB:text> CAVEAT 2 1ABC UNCORRECTABLE AT THIS TIME</RCSB:text> </RCSB:database_PDB_caveat> </RCSB: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 <RCSB:database_PDB_remarkCategory> <RCSB:database_PDB_remark id="3"> <RCSB: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</RCSB:text> </RCSB:database_PDB_remark> <RCSB:database_PDB_remark id="4"> <RCSB: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</RCSB:text> </RCSB:database_PDB_remark> </RCSB: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 <RCSB:database_PDB_revCategory> <RCSB:database_PDB_rev num="1"> <RCSB:author_name>Fitzgerald, Paula M.D</RCSB:author_name> <RCSB:date>1991-10-15</RCSB:date> <RCSB:date_original>1990-04-30</RCSB:date_original> <RCSB:status>full release</RCSB:status> <RCSB:mod_type>0</RCSB:mod_type> </RCSB:database_PDB_rev> </RCSB: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 first PDB record name that was revised. OBSOLETE LOCAL ITEM -- Replaced by attribute type in category database_PDB_rev_record TITLE HEADER COMPND SOURCE The second PDB record name that was revised. OBSOLETE LOCAL ITEM -- Replaced by attribute type in category database_PDB_rev_record TITLE HEADER COMPND SOURCE The third PDB record name that was revised. OBSOLETE LOCAL ITEM -- Replaced by attribute type in category database_PDB_rev_record TITLE HEADER COMPND SOURCE The fourth PDB record name that was revised. OBSOLETE LOCAL ITEM -- Replaced by attribute type in category database_PDB_rev_record TITLE HEADER COMPND SOURCE 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 <RCSB:database_PDB_rev_recordCategory> <RCSB:database_PDB_rev_record rev_num="1" type="CONECT"> <RCSB:details>Error fix - incorrect connection between atoms 2312 and 2317</RCSB:details> </RCSB:database_PDB_rev_record> <RCSB:database_PDB_rev_record rev_num="2" type="MATRIX"> <RCSB:details>For consistency with 1995-08-04 style-guide</RCSB:details> </RCSB:database_PDB_rev_record> <RCSB:database_PDB_rev_record rev_num="3" type="ORIGX"> <RCSB:details>Based on new data from author</RCSB:details> </RCSB:database_PDB_rev_record> </RCSB: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 <RCSB:diffrnCategory> <RCSB:diffrn id="Set1"> <RCSB:ambient_temp>293(3).</RCSB:ambient_temp> <RCSB:ambient_environment> Mother liquor from the reservoir of the vapor diffusion experiment, mounted in room air</RCSB:ambient_environment> <RCSB:crystal_support> 0.7 mm glass capillary, sealed with dental wax</RCSB:crystal_support> <RCSB:crystal_treatment> Equilibrated in rotating anode radiation enclosure for 18 hours prior to beginning of data collection.</RCSB:crystal_treatment> </RCSB:diffrn> </RCSB:diffrnCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. <RCSB:diffrnCategory> <RCSB:diffrn id="d1"> <RCSB: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.</RCSB:details> <RCSB:ambient_temp>293.</RCSB:ambient_temp> </RCSB:diffrn> </RCSB: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]. <RCSB:diffrn_attenuatorCategory> <RCSB:diffrn_attenuator code="1"> <RCSB:scale>16.976</RCSB:scale> </RCSB:diffrn_attenuator> </RCSB: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 <RCSB:diffrn_detectorCategory> <RCSB:diffrn_detector diffrn_id="d1"> <RCSB:detector>multiwire</RCSB:detector> <RCSB:type>Siemens</RCSB:type> </RCSB:diffrn_detector> </RCSB: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 <RCSB:diffrn_measurementCategory> <RCSB:diffrn_measurement diffrn_id="d1"> <RCSB:device>3-circle camera</RCSB:device> <RCSB:device_type>Supper model x</RCSB:device_type> <RCSB:device_details>none</RCSB:device_details> <RCSB:method>omega scan</RCSB:method> <RCSB:details> 440 frames, 0.20 degrees, 150 sec, detector distance 12 cm, detector angle 22.5 degrees</RCSB:details> </RCSB:diffrn_measurement> </RCSB:diffrn_measurementCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. <RCSB:diffrn_measurementCategory> <RCSB:diffrn_measurement diffrn_id="s1"> <RCSB:device_type>Philips PW1100/20 diffractometer</RCSB:device_type> <RCSB:method>\q/2\q</RCSB:method> </RCSB:diffrn_measurement> </RCSB: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 date of data measurement yyyy-mm-dd 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 <RCSB:diffrn_orient_matrixCategory> <RCSB:diffrn_orient_matrix diffrn_id="set1"> <RCSB:type> reciprocal axis matrix, multiplies hkl vector to generate diffractometer xyz vector and diffractometer angles</RCSB:type> <RCSB:UB11>-0.071479</RCSB:UB11> <RCSB:UB12>0.020208</RCSB:UB12> <RCSB:UB13>0.039076</RCSB:UB13> <RCSB:UB21>0.035372</RCSB:UB21> <RCSB:UB22>0.056209</RCSB:UB22> <RCSB:UB23>0.078324</RCSB:UB23> <RCSB:UB31>-0.007470</RCSB:UB31> <RCSB:UB32>0.067854</RCSB:UB32> <RCSB:UB33>-0.017832</RCSB:UB33> </RCSB:diffrn_orient_matrix> </RCSB: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 <RCSB:diffrn_orient_reflnCategory> <RCSB:diffrn_orient_refln diffrn_id="myset1" index_h="2" index_k="0" index_l="2"> <RCSB:angle_chi>-28.45</RCSB:angle_chi> <RCSB:angle_kappa>-11.32</RCSB:angle_kappa> <RCSB:angle_omega>5.33</RCSB:angle_omega> <RCSB:angle_phi>101.78</RCSB:angle_phi> <RCSB:angle_psi>0.00</RCSB:angle_psi> <RCSB:angle_theta>10.66</RCSB:angle_theta> </RCSB:diffrn_orient_refln> </RCSB: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 <RCSB:diffrn_radiationCategory> <RCSB:diffrn_radiation diffrn_id="set1"> <RCSB:collimation>0.3 mm double pinhole</RCSB:collimation> <RCSB:monochromator>graphite</RCSB:monochromator> <RCSB:type>Cu K\a</RCSB:type> <RCSB:wavelength_id>1</RCSB:wavelength_id> </RCSB:diffrn_radiation> </RCSB:diffrn_radiationCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. <RCSB:diffrn_radiationCategory> <RCSB:diffrn_radiation> <RCSB:wavelength_id>1</RCSB:wavelength_id> <RCSB:type>Cu K\a</RCSB:type> <RCSB:monochromator>graphite</RCSB:monochromator> </RCSB:diffrn_radiation> </RCSB: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 Monochromator or Laue. M L 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. SINGLE WAVELENGTH, LAUE, or MAD. SINGLE WAVELENGTH LAUE MAD 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 <RCSB:diffrn_radiation_wavelengthCategory> <RCSB:diffrn_radiation_wavelength id="1"> <RCSB:wavelength>1.54</RCSB:wavelength> <RCSB:wt>1.0</RCSB:wt> </RCSB:diffrn_radiation_wavelength> </RCSB: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 <RCSB:diffrn_reflnCategory> <RCSB:diffrn_refln diffrn_id="set1" id="1102"> <RCSB:wavelength_id>Cu1fixed</RCSB:wavelength_id> <RCSB:angle_chi>32.21</RCSB:angle_chi> <RCSB:angle_kappa>20.12</RCSB:angle_kappa> <RCSB:angle_omega>11.54</RCSB:angle_omega> <RCSB:angle_phi>176.02</RCSB:angle_phi> <RCSB:angle_psi>0.00</RCSB:angle_psi> <RCSB:angle_theta>23.08</RCSB:angle_theta> <RCSB:attenuator_code>Ni.005</RCSB:attenuator_code> <RCSB:counts_bg_1>22</RCSB:counts_bg_1> <RCSB:counts_bg_2>25</RCSB:counts_bg_2> <RCSB:counts_net>3450</RCSB:counts_net> <RCSB:counts_peak>321</RCSB:counts_peak> <RCSB:counts_total>3499</RCSB:counts_total> <RCSB:detect_slit_horiz>0.04</RCSB:detect_slit_horiz> <RCSB:detect_slit_vert>0.02</RCSB:detect_slit_vert> <RCSB:elapsed_time>1.00</RCSB:elapsed_time> <RCSB:index_h>4</RCSB:index_h> <RCSB:index_k>0</RCSB:index_k> <RCSB:index_l>2</RCSB:index_l> <RCSB:intensity_net>202.56</RCSB:intensity_net> <RCSB:intensity_sigma>2.18</RCSB:intensity_sigma> <RCSB:scale_group_code>A24</RCSB:scale_group_code> <RCSB:scan_mode>om</RCSB:scan_mode> <RCSB:scan_mode_backgd>mo</RCSB:scan_mode_backgd> <RCSB:scan_rate>1.2</RCSB:scan_rate> <RCSB:scan_time_backgd>900.00</RCSB:scan_time_backgd> <RCSB:scan_width>1.0</RCSB:scan_width> <RCSB:sint_over_lambda>0.25426</RCSB:sint_over_lambda> <RCSB:standard_code>1</RCSB:standard_code> <RCSB:wavelength>1.54184</RCSB:wavelength> </RCSB:diffrn_refln> </RCSB: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 <RCSB:diffrn_scale_groupCategory> <RCSB:diffrn_scale_group code="A24"> <RCSB:I_net>1.021</RCSB:I_net> </RCSB:diffrn_scale_group> </RCSB: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 <RCSB:diffrn_sourceCategory> <RCSB:diffrn_source diffrn_id="s1"> <RCSB:source>rotating anode</RCSB:source> <RCSB:type>Rigaku RU-200</RCSB:type> <RCSB:power>50kw,180mA.</RCSB:power> <RCSB:target>8mm x 0.4 mm broad-focus</RCSB:target> </RCSB:diffrn_source> </RCSB:diffrn_sourceCategory> The current in milliamperes at which the radiation source was operated. A description of special aspects of the radiation source used. Beamline for synchrotron source. 6A2 7.2 9.5 9.6 A-1 A1 BL-6A BW6 BW7B F-1 F1 PX7.2 PX9.6 UNDULATOR W32 WIGGLER X11 X12C X25 X26-C X31 X4A X8C Synchrotron beamline. Synchrotron site. Yes/No if synchrotron source was used or not. Y N 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]. <RCSB:diffrn_standard_reflnCategory> <RCSB:diffrn_standard_refln diffrn_id="s1" code="1"> <RCSB:index_h>3</RCSB:index_h> <RCSB:index_k>2</RCSB:index_k> <RCSB:index_l>4</RCSB:index_l> </RCSB:diffrn_standard_refln> <RCSB:diffrn_standard_refln diffrn_id="s1" code="1"> <RCSB:index_h>1</RCSB:index_h> <RCSB:index_k>9</RCSB:index_k> <RCSB:index_l>1</RCSB:index_l> </RCSB:diffrn_standard_refln> <RCSB:diffrn_standard_refln diffrn_id="s1" code="1"> <RCSB:index_h>3</RCSB:index_h> <RCSB:index_k>0</RCSB:index_k> <RCSB:index_l>10</RCSB:index_l> </RCSB:diffrn_standard_refln> </RCSB: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]. <RCSB:diffrn_standardsCategory> <RCSB:diffrn_standards diffrn_id="s1"> <RCSB:number>3</RCSB:number> <RCSB:interval_time>120.</RCSB:interval_time> <RCSB:decay_>0.</RCSB:decay_> </RCSB:diffrn_standards> </RCSB: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 EBI_SOLN_SCATTER category record details about a solution scattering experiment Example 1 - based on PDB entry 1HAQ <RCSB:ebi_soln_scatterCategory> <RCSB:ebi_soln_scatter entry_id="1HAQ" id="1"> <RCSB:type>XRAY</RCSB:type> <RCSB:source_type>SRS BEAMLINE 2.1</RCSB:source_type> <RCSB:source_class>synchrotron</RCSB:source_class> <RCSB:source_beamline>2.1</RCSB:source_beamline> <RCSB:detector_type>500-channel quadrant</RCSB:detector_type> <RCSB:temperature>288.</RCSB:temperature> <RCSB:num_time_frames>10</RCSB:num_time_frames> <RCSB:concentration_range>0.7 - 14</RCSB:concentration_range> <RCSB:buffer_name>tris</RCSB:buffer_name> <RCSB:mean_guiner_radius>11.1</RCSB:mean_guiner_radius> <RCSB:mean_guiner_radius_esd>0.4</RCSB:mean_guiner_radius_esd> <RCSB:min_mean_cross_sectional_radii_gyration>4.4</RCSB:min_mean_cross_sectional_radii_gyration> <RCSB:min_mean_cross_sectional_radii_gyration_esd>0.2</RCSB:min_mean_cross_sectional_radii_gyration_esd> <RCSB:max_mean_cross_sectional_radii_gyration>1.7</RCSB:max_mean_cross_sectional_radii_gyration> <RCSB:max_mean_cross_sectional_radii_gyration_esd>0.1</RCSB:max_mean_cross_sectional_radii_gyration_esd> </RCSB:ebi_soln_scatter> <RCSB:ebi_soln_scatter entry_id="1HAQ" id="2"> <RCSB:type>NEUTRON</RCSB:type> <RCSB:source_type>ILL</RCSB:source_type> <RCSB:source_class>neutron source</RCSB:source_class> <RCSB:source_beamline_instrument>D11, D22</RCSB:source_beamline_instrument> <RCSB:detector_type>area</RCSB:detector_type> <RCSB:concentration_range>0.4 - 9.6</RCSB:concentration_range> <RCSB:buffer_name>PBS in 99.9&#37; D2O</RCSB:buffer_name> <RCSB:mean_guiner_radius>11.3</RCSB:mean_guiner_radius> <RCSB:mean_guiner_radius_esd>0.4</RCSB:mean_guiner_radius_esd> <RCSB:min_mean_cross_sectional_radii_gyration>3.9</RCSB:min_mean_cross_sectional_radii_gyration> <RCSB:min_mean_cross_sectional_radii_gyration_esd>0.2</RCSB:min_mean_cross_sectional_radii_gyration_esd> <RCSB:max_mean_cross_sectional_radii_gyration>1.51</RCSB:max_mean_cross_sectional_radii_gyration> <RCSB:max_mean_cross_sectional_radii_gyration_esd>0.06</RCSB:max_mean_cross_sectional_radii_gyration_esd> </RCSB:ebi_soln_scatter> <RCSB:ebi_soln_scatter entry_id="1HAQ" id="3"> <RCSB:type>NEUTRON</RCSB:type> <RCSB:source_type>ISIS</RCSB:source_type> <RCSB:source_class>neutron source</RCSB:source_class> <RCSB:source_beamline>Pulsed Neutron</RCSB:source_beamline> <RCSB:source_beamline_instrument>LOQ</RCSB:source_beamline_instrument> <RCSB:detector_type>AREA (TIME-OF-FLIGHT)</RCSB:detector_type> <RCSB:concentration_range>3.7, 6.1</RCSB:concentration_range> <RCSB:buffer_name>PBS in 99.9&#37; D2O</RCSB:buffer_name> <RCSB:mean_guiner_radius>11.7</RCSB:mean_guiner_radius> <RCSB:mean_guiner_radius_esd>0.5</RCSB:mean_guiner_radius_esd> </RCSB:ebi_soln_scatter> </RCSB:ebi_soln_scatterCategory> The name of the buffer used for the sample in the solution scattering experiment. Acetic acid The concentration range (mg/mL) of the complex in the sample used in the solution scattering experiment to determine the mean radius of structural elongation. 0.7 - 14 A list of the software used in the data analysis SCTPL5, GNOM A list of the software used in the data reduction OTOKO The particular radiation detector. In general this will be a manufacturer, description, model number or some combination of these. The general class of the radiation detector. The maximum mean radius of structural elongation of the sample. In a given solute-solvent contrast, the radius of gyration R_G is a measure of structural elongation if the internal inhomogeneity of scattering densities has no effect. Guiner analysis at low Q give the R_G and the forward scattering at zero angle I(0). lnl(Q) = lnl(0) - R_G^2Q^2/3 where Q = 4(pi)sin(theta/lamda) 2theta = scattering angle lamda = wavelength The above expression is valid in a QR_G range for extended rod-like particles. The relative I(0)/c values ( where c = sample concentration) for sample measurements in a constant buffer for a single sample data session, gives the relative masses of the protein(s) studied when referenced against a standard. see O.Glatter & O.Kratky, (1982). Editors of "Small angle X-ray Scattering, Academic Press, New York. O.Kratky. (1963). X-ray small angle scattering with substances of biological interest in diluted solutions. Prog. Biophys. Chem., 13, 105-173. G.D.Wignall & F.S.Bates, (1987). The small-angle approximation of X-ray and neutron scatter from rigid rods of non-uniform cross section and finite length. J.Appl. Crystallog., 18, 452-460. If the structure is elongated, the mean radius of gyration of the cross-sectional structure R_XS and the mean cross sectional intensity at zero angle [I(Q).Q]_Q->0 is obtained from ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2 The estimated standard deviation for the minimum mean radius of structural elongation of the sample. In a given solute-solvent contrast, the radius of gyration R_G is a measure of structural elongation if the internal inhomogeneity of scattering densities has no effect. Guiner analysis at low Q give the R_G and the forward scattering at zero angle I(0). lnl(Q) = lnl(0) - R_G^2Q^2/3 where Q = 4(pi)sin(theta/lamda) 2theta = scattering angle lamda = wavelength The above expression is valid in a QR_G range for extended rod-like particles. The relative I(0)/c values ( where c = sample concentration) for sample measurements in a constant buffer for a single sample data session, gives the relative masses of the protein(s) studied when referenced against a standard. see O.Glatter & O.Kratky, (1982). Editors of "Small angle X-ray Scattering, Academic Press, New York. O.Kratky. (1963). X-ray small angle scattering with substances of biological interest in diluted solutions. Prog. Biophys. Chem., 13, 105-173. G.D.Wignall & F.S.Bates, (1987). The small-angle approximation of X-ray and neutron scatter from rigid rods of non-uniform cross section and finite length. J.Appl. Crystallog., 18, 452-460. If the structure is elongated, the mean radius of gyration of the cross-sectional structure R_XS and the mean cross sectional intensity at zero angle [I(Q).Q]_Q->0 is obtained from ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2 The mean radius of structural elongation of the sample. In a given solute-solvent contrast, the radius of gyration R_G is a measure of structural elongation if the internal inhomogeneity of scattering densities has no effect. Guiner analysis at low Q give the R_G and the forward scattering at zero angle I(0). lnl(Q) = lnl(0) - R_G^2Q^2/3 where Q = 4(pi)sin(theta/lamda) 2theta = scattering angle lamda = wavelength The above expression is valid in a QR_G range for extended rod-like particles. The relative I(0)/c values ( where c = sample concentration) for sample measurements in a constant buffer for a single sample data session, gives the relative masses of the protein(s) studied when referenced against a standard. see O.Glatter & O.Kratky, (1982). Editors of "Small angle X-ray Scattering, Academic Press, New York. O.Kratky. (1963). X-ray small angle scattering with substances of biological interest in diluted solutions. Prog. Biophys. Chem., 13, 105-173. G.D.Wignall & F.S.Bates, (1987). The small-angle approximation of X-ray and neutron scatter from rigid rods of non-uniform cross section and finite length. J.Appl. Crystallog., 18, 452-460. If the structure is elongated, the mean radius of gyration of the cross-sectional structure R_XS and the mean cross sectional intensity at zero angle [I(Q).Q]_Q->0 is obtained from ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2 The estimated standard deviation for the mean radius of structural elongation of the sample. In a given solute-solvent contrast, the radius of gyration R_G is a measure of structural elongation if the internal inhomogeneity of scattering densities has no effect. Guiner analysis at low Q give the R_G and the forward scattering at zero angle I(0). lnl(Q) = lnl(0) - R_G^2Q^2/3 where Q = 4(pi)sin(theta/lamda) 2theta = scattering angle lamda = wavelength The above expression is valid in a QR_G range for extended rod-like particles. The relative I(0)/c values ( where c = sample concentration) for sample measurements in a constant buffer for a single sample data session, gives the relative masses of the protein(s) studied when referenced against a standard. see O.Glatter & O.Kratky, (1982). Editors of "Small angle X-ray Scattering, Academic Press, New York. O.Kratky. (1963). X-ray small angle scattering with substances of biological interest in diluted solutions. Prog. Biophys. Chem., 13, 105-173. G.D.Wignall & F.S.Bates, (1987). The small-angle approximation of X-ray and neutron scatter from rigid rods of non-uniform cross section and finite length. J.Appl. Crystallog., 18, 452-460. If the structure is elongated, the mean radius of gyration of the cross-sectional structure R_XS and the mean cross sectional intensity at zero angle [I(Q).Q]_Q->0 is obtained from ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2 The minimum mean radius of structural elongation of the sample. In a given solute-solvent contrast, the radius of gyration R_G is a measure of structural elongation if the internal inhomogeneity of scattering densities has no effect. Guiner analysis at low Q give the R_G and the forward scattering at zero angle I(0). lnl(Q) = lnl(0) - R_G^2Q^2/3 where Q = 4(pi)sin(theta/lamda) 2theta = scattering angle lamda = wavelength The above expression is valid in a QR_G range for extended rod-like particles. The relative I(0)/c values ( where c = sample concentration) for sample measurements in a constant buffer for a single sample data session, gives the relative masses of the protein(s) studied when referenced against a standard. see O.Glatter & O.Kratky, (1982). Editors of "Small angle X-ray Scattering, Academic Press, New York. O.Kratky. (1963). X-ray small angle scattering with substances of biological interest in diluted solutions. Prog. Biophys. Chem., 13, 105-173. G.D.Wignall & F.S.Bates, (1987). The small-angle approximation of X-ray and neutron scatter from rigid rods of non-uniform cross section and finite length. J.Appl. Crystallog., 18, 452-460. If the structure is elongated, the mean radius of gyration of the cross-sectional structure R_XS and the mean cross sectional intensity at zero angle [I(Q).Q]_Q->0 is obtained from ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2 The estimated standard deviation for the minimum mean radius of structural elongation of the sample. In a given solute-solvent contrast, the radius of gyration R_G is a measure of structural elongation if the internal inhomogeneity of scattering densities has no effect. Guiner analysis at low Q give the R_G and the forward scattering at zero angle I(0). lnl(Q) = lnl(0) - R_G^2Q^2/3 where Q = 4(pi)sin(theta/lamda) 2theta = scattering angle lamda = wavelength The above expression is valid in a QR_G range for extended rod-like particles. The relative I(0)/c values ( where c = sample concentration) for sample measurements in a constant buffer for a single sample data session, gives the relative masses of the protein(s) studied when referenced against a standard. see O.Glatter & O.Kratky, (1982). Editors of "Small angle X-ray Scattering, Academic Press, New York. O.Kratky. (1963). X-ray small angle scattering with substances of biological interest in diluted solutions. Prog. Biophys. Chem., 13, 105-173. G.D.Wignall & F.S.Bates, (1987). The small-angle approximation of X-ray and neutron scatter from rigid rods of non-uniform cross section and finite length. J.Appl. Crystallog., 18, 452-460. If the structure is elongated, the mean radius of gyration of the cross-sectional structure R_XS and the mean cross sectional intensity at zero angle [I(Q).Q]_Q->0 is obtained from ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2 The number of time frame solution scattering imgaes used. The pH value of the buffered sample. The length (or range) of the protein sample under study. If the solution structure is approximated as an elongated elliptical cyclinder the the length L is determined from, L = sqrt [12( (R_G)^2 - (R_XS)^2 ) ] The length should also be given by L = pi I(0) / [ I(Q).Q]_Q->0 The beamline used for the experiment The instrumentation used on the beamline The general class of the radiation source. neutron source synchrotron The make, model, name or beamline of the source of radiation. The temperature in kelvins at which the experiment was conducted The type of solution scattering experiment carried out This data item is a pointer to attribute id in category entry in the ENTRY category. The value of attribute id in category ebi_soln_scatter must uniquely identify the sample in the category EBI_SOLN_SCATTER Data items in the EBI_SOLN_SCATTER_MODEL category record details about a homology model fitting to the solution scatter data A description of the conformer selection criteria used. THE MODELLED SCATTERING CURVES WERE ASSESSED BY CALCULATION OF THE RG, RSX-1 AND RXS-2 VALUES IN THE SAME Q RANGES USED IN THE EXPERIMENTAL GUINIER FITS. MODELS WERE THEN RANKED USING A GOODNESS-OF-FIT R-FACTOR DEFINED BY ANALOGY WITH PROTEIN CRYSTALLOGRAPHY AND BASED ON THE EXPERIMENTAL CURVES IN THE Q RANGE EXTENDING TO 1.4 NM-1. A description of any additional details concerning the experiment. HOMOLOGY MODELS WERE BUILT FOR THE 17 SCR DOMAINS AND ENERGY MINIMISATIONS WERE PERFORMED TO IMPROVE THE CONNECTIVITY IN THE FH MODEL. TRIANTENNARY COMPLEX-TYPE CARBOHYDRATE STRUCTURES (MAN3GLCNAC6GAL3FUC3NEUNAC1) WERE ADDED TO EACH OF THE N-LINKED GLYCOSYLATION SITES. A LIBRARY OF LINKER PEPTIDE CONFORMATIONS WAS USED IN DOMAIN MODELLING CONSTRAINED BY THE SOLUTION SCATTERING FITS. MODELLING WITH THE SCATTERING DATA WAS ALSO CARRIED OUT BY ROTATIONAL SEARCH METHODS. THE X-RAY AND NEUTRON SCATTERING CURVE I(Q) WAS CALCULATED ASSUMING A UNIFORM SCATTERING DENSITY FOR THE SPHERES USING THE DEBYE EQUATION AS ADAPTED TO SPHERES. X-RAY CURVES WERE CALCULATED FROM THE HYDRATED SPHERE MODELS WITHOUT CORRECTIONS FOR WAVELENGTH SPREAD OR BEAM DIVERGENCE, WHILE THESE CORRECTIONS WERE APPLIED FOR THE NEUTRON CURVES BUT NOW USING UNHYDRATED MODELS. A list of the entries used to fit the model to the scattering data PDB CODE 1HFI, 1HCC, 1HFH, 1VCC A description of the methods used in the modelling CONSTRAINED SCATTERING FITTING OF HOMOLOGY MODELS The number of model conformers calculated. The number of model conformers submitted in the entry A list of the software authors MSI A list of the software used in the modeeling INSIGHT II, HOMOLOGY, DISCOVERY, BIOPOLYMER, DELPHI The value of attribute id in category ebi_soln_scatter_model must uniquely identify the sample in the category EBI_SOLN_SCATTER_MODEL This data item is a pointer to attribute id in category ebi_soln_scatter in the EBI_SOLN_SCATTER category. Data items in the EBI_VALIDATE_ANGLE category list the the covalent bond angles found in an entry that have values which deviate from expected values by more than 6*rmsd for the particular entry from the expected standard value Example 1 - based on PDB entry 1DWW <RCSB:ebi_validate_angleCategory> <RCSB:ebi_validate_angle id="1"> <RCSB:model_id>1</RCSB:model_id> <RCSB:auth_asym_id_1>A</RCSB:auth_asym_id_1> <RCSB:auth_atom_id_1> CA </RCSB:auth_atom_id_1> <RCSB:auth_comp_id_1>LEU</RCSB:auth_comp_id_1> <RCSB:auth_seq_id_1>110</RCSB:auth_seq_id_1> <RCSB:auth_asym_id_2>A</RCSB:auth_asym_id_2> <RCSB:auth_atom_id_2> CB </RCSB:auth_atom_id_2> <RCSB:auth_comp_id_2>LEU</RCSB:auth_comp_id_2> <RCSB:auth_seq_id_2>110</RCSB:auth_seq_id_2> <RCSB:auth_asym_id_3>A</RCSB:auth_asym_id_3> <RCSB:auth_atom_id_3> CG </RCSB:auth_atom_id_3> <RCSB:auth_comp_id_3>LEU</RCSB:auth_comp_id_3> <RCSB:auth_seq_id_3>110</RCSB:auth_seq_id_3> <RCSB:angle_deviation>8.6</RCSB:angle_deviation> </RCSB:ebi_validate_angle> <RCSB:ebi_validate_angle id="2"> <RCSB:model_id>1</RCSB:model_id> <RCSB:auth_asym_id_1>A</RCSB:auth_asym_id_1> <RCSB:auth_atom_id_1> N </RCSB:auth_atom_id_1> <RCSB:auth_comp_id_1>GLY</RCSB:auth_comp_id_1> <RCSB:auth_seq_id_1>122</RCSB:auth_seq_id_1> <RCSB:auth_asym_id_2>A</RCSB:auth_asym_id_2> <RCSB:auth_atom_id_2> CA </RCSB:auth_atom_id_2> <RCSB:auth_comp_id_2>GLY</RCSB:auth_comp_id_2> <RCSB:auth_seq_id_2>122</RCSB:auth_seq_id_2> <RCSB:auth_asym_id_3>A</RCSB:auth_asym_id_3> <RCSB:auth_atom_id_3> C </RCSB:auth_atom_id_3> <RCSB:auth_comp_id_3>GLY</RCSB:auth_comp_id_3> <RCSB:auth_seq_id_3>122</RCSB:auth_seq_id_3> <RCSB:angle_deviation>8.3</RCSB:angle_deviation> </RCSB:ebi_validate_angle> <RCSB:ebi_validate_angle id="3"> <RCSB:model_id>1</RCSB:model_id> <RCSB:auth_asym_id_1>A</RCSB:auth_asym_id_1> <RCSB:auth_atom_id_1> N </RCSB:auth_atom_id_1> <RCSB:auth_comp_id_1>THR</RCSB:auth_comp_id_1> <RCSB:auth_seq_id_1>176</RCSB:auth_seq_id_1> <RCSB:auth_asym_id_2>A</RCSB:auth_asym_id_2> <RCSB:auth_atom_id_2> CA </RCSB:auth_atom_id_2> <RCSB:auth_comp_id_2>THR</RCSB:auth_comp_id_2> <RCSB:auth_seq_id_2>176</RCSB:auth_seq_id_2> <RCSB:auth_asym_id_3>A</RCSB:auth_asym_id_3> <RCSB:auth_atom_id_3> C </RCSB:auth_atom_id_3> <RCSB:auth_comp_id_3>THR</RCSB:auth_comp_id_3> <RCSB:auth_seq_id_3>176</RCSB:auth_seq_id_3> <RCSB:angle_deviation>-8.1</RCSB:angle_deviation> </RCSB:ebi_validate_angle> <RCSB:ebi_validate_angle id="4"> <RCSB:model_id>1</RCSB:model_id> <RCSB:auth_asym_id_1>A</RCSB:auth_asym_id_1> <RCSB:auth_atom_id_1> N </RCSB:auth_atom_id_1> <RCSB:auth_comp_id_1>ARG</RCSB:auth_comp_id_1> <RCSB:auth_seq_id_1>197</RCSB:auth_seq_id_1> <RCSB:auth_asym_id_2>A</RCSB:auth_asym_id_2> <RCSB:auth_atom_id_2> CA </RCSB:auth_atom_id_2> <RCSB:auth_comp_id_2>ARG</RCSB:auth_comp_id_2> <RCSB:auth_seq_id_2>197</RCSB:auth_seq_id_2> <RCSB:auth_asym_id_3>A</RCSB:auth_asym_id_3> <RCSB:auth_atom_id_3> C </RCSB:auth_atom_id_3> <RCSB:auth_comp_id_3>ARG</RCSB:auth_comp_id_3> <RCSB:auth_seq_id_3>197</RCSB:auth_seq_id_3> <RCSB:angle_deviation>10.7</RCSB:angle_deviation> </RCSB:ebi_validate_angle> <RCSB:ebi_validate_angle id="5"> <RCSB:model_id>1</RCSB:model_id> <RCSB:auth_asym_id_1>A</RCSB:auth_asym_id_1> <RCSB:auth_atom_id_1> N </RCSB:auth_atom_id_1> <RCSB:auth_comp_id_1>PHE</RCSB:auth_comp_id_1> <RCSB:auth_seq_id_1>251</RCSB:auth_seq_id_1> <RCSB:auth_asym_id_2>A</RCSB:auth_asym_id_2> <RCSB:auth_atom_id_2> CA </RCSB:auth_atom_id_2> <RCSB:auth_comp_id_2>PHE</RCSB:auth_comp_id_2> <RCSB:auth_seq_id_2>251</RCSB:auth_seq_id_2> <RCSB:auth_asym_id_3>A</RCSB:auth_asym_id_3> <RCSB:auth_atom_id_3> C </RCSB:auth_atom_id_3> <RCSB:auth_comp_id_3>PHE</RCSB:auth_comp_id_3> <RCSB:auth_seq_id_3>251</RCSB:auth_seq_id_3> <RCSB:angle_deviation>-9.3</RCSB:angle_deviation> </RCSB:ebi_validate_angle> </RCSB:ebi_validate_angleCategory> Value of the deviation (in degrees) from 6*RMSD for the Angle bounded by the three sites from the expected dictionary value identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. Optional identifier of the first of the three atom sites that define the angle. Optional identifier of the second of the three atom sites that define the angle. Optional identifier of the third of the three atom sites that define the angle. The model number for the given angle The value of attribute id in category ebi_validate_angle must uniquely identify each item in the EBI_VALIDATE_ANGLE list. This is an integer serial number. Data items in the EBI_VALIDATE_BOND category list the covalent bonds that have values which deviate from expected values by more than 6*rmsd. Example 1 - based on PDB entry 1DX2 <RCSB:ebi_validate_bondCategory> <RCSB:ebi_validate_bond id="1"> <RCSB:model_id>1</RCSB:model_id> <RCSB:auth_asym_id_1>L</RCSB:auth_asym_id_1> <RCSB:auth_atom_id_1>CA </RCSB:auth_atom_id_1> <RCSB:auth_comp_id_1>THR</RCSB:auth_comp_id_1> <RCSB:auth_seq_id_1>17</RCSB:auth_seq_id_1> <RCSB:auth_asym_id_2>L</RCSB:auth_asym_id_2> <RCSB:auth_atom_id_2>CB </RCSB:auth_atom_id_2> <RCSB:auth_comp_id_2>THR</RCSB:auth_comp_id_2> <RCSB:auth_seq_id_2>17</RCSB:auth_seq_id_2> <RCSB:bond_deviation>0.39</RCSB:bond_deviation> </RCSB:ebi_validate_bond> <RCSB:ebi_validate_bond id="2"> <RCSB:model_id>1</RCSB:model_id> <RCSB:auth_asym_id_1>L</RCSB:auth_asym_id_1> <RCSB:auth_atom_id_1>CA </RCSB:auth_atom_id_1> <RCSB:auth_comp_id_1>ILE</RCSB:auth_comp_id_1> <RCSB:auth_seq_id_1>111</RCSB:auth_seq_id_1> <RCSB:auth_asym_id_2>L</RCSB:auth_asym_id_2> <RCSB:auth_atom_id_2>CB </RCSB:auth_atom_id_2> <RCSB:auth_comp_id_2>ILE</RCSB:auth_comp_id_2> <RCSB:auth_seq_id_2>111</RCSB:auth_seq_id_2> <RCSB:bond_deviation>0.31</RCSB:bond_deviation> </RCSB:ebi_validate_bond> <RCSB:ebi_validate_bond id="3"> <RCSB:model_id>1</RCSB:model_id> <RCSB:auth_asym_id_1>H</RCSB:auth_asym_id_1> <RCSB:auth_atom_id_1>CA </RCSB:auth_atom_id_1> <RCSB:auth_comp_id_1>ALA</RCSB:auth_comp_id_1> <RCSB:auth_seq_id_1>192</RCSB:auth_seq_id_1> <RCSB:auth_asym_id_2>H</RCSB:auth_asym_id_2> <RCSB:auth_atom_id_2>CB </RCSB:auth_atom_id_2> <RCSB:auth_comp_id_2>ALA</RCSB:auth_comp_id_2> <RCSB:auth_seq_id_2>192</RCSB:auth_seq_id_2> <RCSB:bond_deviation>-0.16</RCSB:bond_deviation> </RCSB:ebi_validate_bond> </RCSB:ebi_validate_bondCategory> An optional identifier of the first of the two atoms that define the covalent bond. This data item is a pointer to attribute id in category atom_sites_alt in the ATOM_SITE category. An optional identifier of the second of the two atoms that define the covalent bond. This data item is a pointer to attribute id in category atom_sites_alt in the ATOM_SITE category. identifier of the first of the two atom sites that define the covalent bond. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. identifier of the second of the two atom sites that define the covalent bond. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. identifier of the first of the two atom sites that define the covalent bond. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. identifier of the second of the two atom sites that define the covalent bond. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. identifier of the first of the two atom sites that define the covalent bond. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. identifier of the second of the two atom sites that define the covalent bond. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. identifier of the first of the two atom sites that define the covalent bond. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. identifier of the second of the two atom sites that define the covalent bond. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. The value of the deviation from ideal for the defined covalent bond for the two atoms defined. Optional identifier of the first of the two atom sites that define the covalent bond. Optional identifier of the second of the two atom sites that define the covalent bond. The model number for the given bond The value of attribute id in category ebi_validate_bond must uniquely identify each item in the EBI_VALIDATE_BOND list. This is an integer serial number. Data items in the EBI_VALIDATE_CHIRAL category list the residues that contain unexpected configuration of chiral centres. identifier of the residue This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. identifier of the residue This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. identifier of the residue This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. A description of the outlier angle e.g. ALPHA-CARBON Optional identifier of the residue The model number for the given residue The value of the OMEGA angle for the peptide linkage between the two defined residues The value of attribute id in category ebi_validate_chiral must uniquely identify each item in the EBI_VALIDATE_CHIRAL list. This is an integer serial number. Data items in the EBI_VALIDATE_CONTACT category list the atoms within the entry that are in close contact with regard the distances expected from either covalent bonding or closest approach by van der Waals contacts. Both contacts with the asymmetric unit and symmetry related contacts are considered. For those contacts not involving hydrogen a limit of 2.2 Angstroms is used. For contacts involving a hydrogen atom a cutoff of 1.6Angstrom is used. Example 1 - based on PDB entry 1DZW <RCSB:ebi_validate_contactCategory> <RCSB:ebi_validate_contact id="1"> <RCSB:model_id>1</RCSB:model_id> <RCSB:auth_atom_id_1> O </RCSB:auth_atom_id_1> <RCSB:auth_asym_id_1>W</RCSB:auth_asym_id_1> <RCSB:auth_comp_id_1>HOH</RCSB:auth_comp_id_1> <RCSB:auth_seq_id_1>101</RCSB:auth_seq_id_1> <RCSB:auth_atom_id_2> O </RCSB:auth_atom_id_2> <RCSB:auth_asym_id_2>W</RCSB:auth_asym_id_2> <RCSB:auth_comp_id_2>HOH</RCSB:auth_comp_id_2> <RCSB:auth_seq_id_2>101</RCSB:auth_seq_id_2> <RCSB:dist>1.0</RCSB:dist> </RCSB:ebi_validate_contact> </RCSB:ebi_validate_contactCategory> An optional identifier of the first of the two atoms that define the close contact. This data item is a pointer to attribute id in category atom_sites_alt in the ATOM_SITE category. An optional identifier of the second of the two atoms that define the close contact. This data item is a pointer to attribute id in category atom_sites_alt in the ATOM_SITE category. identifier of the first of the two atom sites that define the close contact. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. identifier of the second of the two atom sites that define the close contact. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. identifier of the first of the two atom sites that define the close contact. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. identifier of the second of the two atom sites that define the close contact. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. identifier of the first of the two atom sites that define the close contact. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. identifier of the second of the two atom sites that define the close contact. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. identifier of the first of the two atom sites that define the close contact. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. identifier of the second of the two atom sites that define the close contact. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. The value of the close contact for the two atoms defined. Optional identifier of the first of the two atom sites that define the close contact. Optional identifier of the second of the two atom sites that define the close contact. The model number for the given angle The symmetry of the first of the two atoms define the close contact. The Symmetry equivalent position is given in the 'xyz' representation. The symmetry of the second of the two atoms define the close contact. The Symmetry equivalent position is given in the 'xyz' representation. The value of attribute id in category ebi_validate_contact must uniquely identify each item in the EBI_VALIDATE_CONTACT list. This is an integer serial number. Data items in the EBI_VALIDATE_PEPTIDE_OMEGA category list the residues that contain peptide bonds deviate significantly from both cis and trans conformation. cis bonds, if any, are listed on cispep records. trans is defined as 180 +/- 30 and cis is defined as 0 +/- 30 degrees. Example 1 - based on PDB entry 1E3V <RCSB:ebi_validate_peptide_omegaCategory> <RCSB:ebi_validate_peptide_omega id="1"> <RCSB:model_id>1</RCSB:model_id> <RCSB:auth_comp_id_1>LEU</RCSB:auth_comp_id_1> <RCSB:auth_asym_id_1>B</RCSB:auth_asym_id_1> <RCSB:auth_seq_id_1>61</RCSB:auth_seq_id_1> <RCSB:auth_comp_id_2>GLY</RCSB:auth_comp_id_2> <RCSB:auth_asym_id_2>B</RCSB:auth_asym_id_2> <RCSB:auth_seq_id_2>62</RCSB:auth_seq_id_2> <RCSB:omega>134.62</RCSB:omega> </RCSB:ebi_validate_peptide_omega> <RCSB:ebi_validate_peptide_omega id="2"> <RCSB:model_id>1</RCSB:model_id> <RCSB:auth_comp_id_1>GLY</RCSB:auth_comp_id_1> <RCSB:auth_asym_id_1>B</RCSB:auth_asym_id_1> <RCSB:auth_seq_id_1>64</RCSB:auth_seq_id_1> <RCSB:auth_comp_id_2>LYS</RCSB:auth_comp_id_2> <RCSB:auth_asym_id_2>B</RCSB:auth_asym_id_2> <RCSB:auth_seq_id_2>65</RCSB:auth_seq_id_2> <RCSB:omega>127.65</RCSB:omega> </RCSB:ebi_validate_peptide_omega> </RCSB:ebi_validate_peptide_omegaCategory> identifier of the first residue in the bond This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. identifier of the second residue in the bond This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. identifier of the first residue in the bond This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. identifier of the second residue in the bond This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. identifier of the first residue in the bond This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. identifier of the second residue in the bond This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. Optional identifier of the first residue in the bond Optional identifier of the second residue in the bond The model number for the given residue The value of the OMEGA angle for the peptide linkage between the two defined residues The value of attribute id in category ebi_validate_peptide_omega must uniquely identify each item in the EBI_VALIDATE_PEPTIDE_OMEGA list. This is an integer serial number. Data items in the EBI_VALIDATE_TORSION category list the residues with torsion angles outside the expected ramachandran regions Example 1 - based on PDB entry 1E3J <RCSB:ebi_validate_torsionCategory> <RCSB:ebi_validate_torsion id="1"> <RCSB:model_id>1</RCSB:model_id> <RCSB:auth_comp_id>ALA</RCSB:auth_comp_id> <RCSB:auth_asym_id>A</RCSB:auth_asym_id> <RCSB:auth_seq_id>54</RCSB:auth_seq_id> <RCSB:phi>174.28</RCSB:phi> <RCSB:psi>-125.91</RCSB:psi> </RCSB:ebi_validate_torsion> <RCSB:ebi_validate_torsion id="2"> <RCSB:model_id>1</RCSB:model_id> <RCSB:auth_comp_id>ARG</RCSB:auth_comp_id> <RCSB:auth_asym_id>A</RCSB:auth_asym_id> <RCSB:auth_seq_id>296</RCSB:auth_seq_id> <RCSB:phi>62.27</RCSB:phi> <RCSB:psi>-118.17</RCSB:psi> </RCSB:ebi_validate_torsion> </RCSB:ebi_validate_torsionCategory> identifier of the residue This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. identifier of the residue This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. identifier of the residue This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. Optional identifier of the residue The model number for the given residue The Phi value that for the residue that lies outside normal limits (in combination with the Psi value) with regards the rammachandran plot The Psi value that for the residue that lies outside normal limits (in combination with the Phi value) with regards the rammachandran plot The value of attribute id in category ebi_validate_torsion must uniquely identify each item in the EBI_VALIDATE_TORSION list. This is an integer serial number. 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 <RCSB:em_2d_crystal_growCategory> <RCSB:em_2d_crystal_grow id="1"> <RCSB:atmosphere>room air</RCSB:atmosphere> <RCSB:pH>5.2</RCSB:pH> <RCSB:temp>18.</RCSB:temp> <RCSB:buffer_id>2</RCSB:buffer_id> <RCSB:details>on grid</RCSB:details> <RCSB:number_2d_crystals>129</RCSB:number_2d_crystals> <RCSB:citation_id>2</RCSB:citation_id> </RCSB:em_2d_crystal_grow> </RCSB: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 <RCSB:em_2d_projection_selectionCategory> <RCSB:em_2d_projection_selection entry_id="1"> <RCSB:software_name>1</RCSB:software_name> <RCSB:method>INTERACTIVE</RCSB:method> <RCSB:citation_id>1</RCSB:citation_id> </RCSB:em_2d_projection_selection> </RCSB: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 <RCSB:em_3d_fittingCategory> <RCSB:em_3d_fitting id="1" entry_id="1DYL"> <RCSB:method>AUTOMATIC</RCSB:method> <RCSB:target_criteria>R-FACTOR</RCSB:target_criteria> <RCSB:software_name>1</RCSB:software_name> <RCSB:ref_space>REAL</RCSB:ref_space> <RCSB:ref_protocol>RIGID BODY REFINEMENT</RCSB:ref_protocol> <RCSB: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. </RCSB:details> </RCSB:em_3d_fitting> </RCSB: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 <RCSB:em_3d_fitting_listCategory> <RCSB:em_3d_fitting_list id="1"> <RCSB:pdb_entry_id>1VCQ</RCSB:pdb_entry_id> </RCSB:em_3d_fitting_list> </RCSB: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 <RCSB:em_3d_reconstructionCategory> <RCSB:em_3d_reconstruction entry_id="1DYL" id="1"> <RCSB:method>CROSS-COMMON LINES</RCSB:method> <RCSB:citation_id>1</RCSB:citation_id> <RCSB:resolution>9.</RCSB:resolution> <RCSB:nominal_pixel_size>2.64</RCSB:nominal_pixel_size> <RCSB:actual_pixel_size>2.52</RCSB:actual_pixel_size> </RCSB:em_3d_reconstruction> </RCSB: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 <RCSB:em_assemblyCategory> <RCSB:em_assembly id="1" entry_id="1DYL"> <RCSB:name>virus</RCSB:name> <RCSB:aggregation_state>icosahedral</RCSB:aggregation_state> <RCSB:composition>virus</RCSB:composition> <RCSB:num_components>1</RCSB:num_components> </RCSB:em_assembly> </RCSB:em_assemblyCategory> A description of the aggregation state of the assembly. SINGLE PARTICLE INDIVIDUAL STRUCTURE 2D-CRYSTAL ICOSAHEDRAL HELICAL FILAMENT HELICAL FILAMENTS TISSUE 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 <RCSB:em_buffer_componentsCategory> <RCSB:em_buffer_components buffer_id="1" id="1"> <RCSB:name>NaCl</RCSB:name> <RCSB:volume>0.200 </RCSB:volume> <RCSB:conc>4 </RCSB:conc> </RCSB:em_buffer_components> <RCSB:em_buffer_components buffer_id="1" id="2"> <RCSB:name>Acetic Acid</RCSB:name> <RCSB:volume>0.047 </RCSB:volume> <RCSB:conc>100</RCSB:conc> </RCSB:em_buffer_components> <RCSB:em_buffer_components buffer_id="1" id="3"> <RCSB:name>water</RCSB:name> <RCSB:volume>0.700 </RCSB:volume> <RCSB:conc>neat</RCSB:conc> </RCSB:em_buffer_components> </RCSB: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 <RCSB:em_detectorCategory> <RCSB:em_detector entry_id="1DYL" id="1"> <RCSB:type>KODAK SO163 FILM</RCSB:type> </RCSB:em_detector> </RCSB: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. KODAK SO163 FILM GATAN 673 GATAN 676 GATAN 692 GATAN 794 GATAN 1000 GATAN 4000 TVIPS BIOCAM TVIPS TEMCAM F214 TVIPS TEMCAM F224 TVIPS FASTSCAN F114 PROSCAN AMT 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_ELECTRON_DIFFRACTION category record details about the electron diffraction data from the electron crystallography experiment. Example 1 - based on PDB entry 1TUB and laboratory records for the structure corresponding to PDB entry 1TUB <RCSB:em_electron_diffractionCategory> <RCSB:em_electron_diffraction entry_id="1TUB" id="1"> <RCSB:num_structure_factors>12000</RCSB:num_structure_factors> <RCSB:details xsi:nil="true" /> </RCSB:em_electron_diffraction> </RCSB:em_electron_diffractionCategory> Details of the electron diffraction experiment THE MODEL WAS DERIVED USING ELECTRON DIFFRACTION AND IMAGE DATA FROM TWO DIMENSIONAL CRYSTALS OF TUBULIN INDUCED BY THE PRESENCE OF ZN++ IONS. WHAT FOLLOWS ARE THE COORDINATES FOR THE AB-TUBULIN DIMER BOUND TO TAXOL AS OBTAINED BY ELECTRON CRYSTALLOGRAPHY OF ZINC-INDUCED SHEETS. THIS IS THE UNREFINED MODEL, BUILT INTO A RAW DENSITY MAP WHERE THE RESOLUTION IN THE PLANE OF THE SHEET WAS 3.7 ANGSTROMS AND THAT PERPENDICULAR TO THE SHEET ABOUT 4.8 ANGSTROMS. THE MODEL DOES NOT CONTAIN MOST OF THE C-TERMINAL RESIDUES OF EITHER MONOMER WHICH WERE DISORDERED IN THE MAP. THE LOOP BETWEEN HELIX H1 AND STRAND S2, AND THAT BETWEEN H2 AND S3 ARE PRESENT FOR COMPLETENESS BUT WERE BUILT INTO VERY WEAK DENSITY. GIVEN THE LIMITED RESOLUTION OF THE MAP, THE CONFORMATION OF THE SIDE CHAINS, ESPECIALLY THOSE CORRESPONDING TO RESIDUES ON THE SURFACE OF THE DIMER, MUST BE TAKEN CAUTIOUSLY. IN ADDITION, BECAUSE THIS IS AN UNREFINED MODEL, CERTAIN GEOMETRY ERRORS MAY STILL BE PRESENT IN THE STRUCTURE. PLEASE TAKE THIS INTO ACCOUNT WHEN INTERPRETING YOUR OWN DATA BASED ON THE PRESENT TUBULIN STRUCTURE. ALTHOUGH THE POSITION OF RESIDUES (WITH THE EXCEPTION OF THOSE IN THE LOOPS MENTIONED ABOVE) SHOULD NOT CHANGE SIGNIFICANTLY UPON REFINEMENT, DRAWING INFORMATION AT THE LEVEL OF SIDE CHAIN CONFORMATION IS CLEARLY NOT ADVISED. FINALLY, PLEASE NOTICE THAT THE TAXOID IN THE MODEL IS THE TAXOL DERIVATIVE TAXOTERE. 1 The number of diffraction patterns used from the electron diffraction experiment. The number of structure factors from the electron diffraction experiment. 12000 The value of attribute id in category electron_diffraction must uniquely identify the electron diffraction experiment. This data item is a pointer to attribute id in category entry in the ENTRY category. data items in the em_electron_diffraction_pattern category record details about the pattern information from the electron diffraction experiment. example 1 - based on pdb entry 1tub and laboratory records for the structure corresponding to pdb entry 1tub <RCSB:em_electron_diffraction_patternCategory> <RCSB:em_electron_diffraction_pattern entry_id="1TUB" id="1"> <RCSB:num_patterns_by_tilt_angle>1</RCSB:num_patterns_by_tilt_angle> <RCSB:num_images_by_tilt_angle>4</RCSB:num_images_by_tilt_angle> </RCSB:em_electron_diffraction_pattern> </RCSB:em_electron_diffraction_patternCategory> the number of images by tilt angle. 4 the number of diffraction patterns by tilt angle. 1 the tilt angle at which the diffraction pattern was obtained. the value of attribute id in category electron_diffraction_pattern must uniquely identify the electron diffraction pattern experiment. this data item is a pointer to attribute id in category entry in the entry category. data items in the em_electron_diffraction_phase category record details about the phase information from the electron diffraction experiment. example 1 - based on pdb entry 1tub and laboratory records for the structure corresponding to pdb entry 1tub <RCSB:em_electron_diffraction_phaseCategory> <RCSB:em_electron_diffraction_phase entry_id="1TUB" id="1"> <RCSB:d_res_high>4.0</RCSB:d_res_high> </RCSB:em_electron_diffraction_phase> </RCSB:em_electron_diffraction_phaseCategory> the highest resolution d-value for the electron diffraction experiment. 5.0 the highest resolution shell error in degrees. the overall phase error in degrees. the rejection criteria (phase error) in degrees. the phase residual value for the electron diffraction experiment. the value of attribute id in category electron_diffraction_phase must uniquely identify the electron diffraction phase experiment. this data item is a pointer to attribute id in category entry in the entry category. 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 <RCSB:em_entity_assemblyCategory> <RCSB:em_entity_assembly id="1" assembly_id="1"> <RCSB:type>VIRUS</RCSB:type> </RCSB:em_entity_assembly> </RCSB: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 <RCSB:em_entity_assembly_listCategory> <RCSB:em_entity_assembly_list entity_assembly_id="1" id="1" entity_id="1"> <RCSB:oligomeric_details>DIMER</RCSB:oligomeric_details> <RCSB:number_of_copies>2</RCSB:number_of_copies> </RCSB:em_entity_assembly_list> </RCSB: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 <RCSB:em_icos_virus_shellsCategory> <RCSB:em_icos_virus_shells virus_entity_id="1" id="1"> <RCSB:shell_diameter>400.</RCSB:shell_diameter> <RCSB:triangulation_num>4</RCSB:triangulation_num> </RCSB:em_icos_virus_shells> </RCSB: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 <RCSB:em_image_scansCategory> <RCSB:em_image_scans entry_id="1DYL" id="2"> <RCSB:number_digital_images>48</RCSB:number_digital_images> <RCSB:citation_id>1</RCSB:citation_id> </RCSB:em_image_scans> </RCSB: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 <RCSB:em_imagingCategory> <RCSB:em_imaging entry_id="1DYL" id="1"> <RCSB:sample_support_id>1</RCSB:sample_support_id> <RCSB:microscope_model>FEI/PHILIPS CM200 FEG</RCSB:microscope_model> <RCSB:specimen_holder_type>cryotransfer</RCSB:specimen_holder_type> <RCSB:specimen_holder_model>gatan 626-0300</RCSB:specimen_holder_model> <RCSB:date>1998-15-06</RCSB:date> <RCSB:accelerating_voltage>200</RCSB:accelerating_voltage> <RCSB:illumination_mode>bright field</RCSB:illumination_mode> <RCSB:mode>low dose</RCSB:mode> <RCSB:nominal_cs>2.0</RCSB:nominal_cs> <RCSB:nominal_defocus_min>975.</RCSB:nominal_defocus_min> <RCSB:nominal_defocus_max>7600.</RCSB:nominal_defocus_max> <RCSB:tilt_angle_min>0.</RCSB:tilt_angle_min> <RCSB:tilt_angle_max>0.</RCSB:tilt_angle_max> <RCSB:nominal_magnification>50000</RCSB:nominal_magnification> <RCSB:electron_source>FEG</RCSB:electron_source> <RCSB:citation_id>1</RCSB:citation_id> <RCSB:temperature>95.</RCSB:temperature> </RCSB:em_imaging> </RCSB: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 or the date at which a series of experiments began. 2001-05-08 Any additional imaging details. weak beam illumination The camera length (in millimetres). 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. FIELD EMISSION GUN LAB6 TUNGSTEN HAIRPIN SCHOTTKY FIELD EMISSION GUN OTHER 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. FLOOD BEAM FLOOD BEAM LOW DOSE SPOT SCAN OTHER The name of the model of microscope. HITACHI H8100 HITACHI HF2000 HITACHI HF2000-UHR HITACHI H9000-UHR HITACHI H9000-NAR HITACHI 300KEV FEG HITACHI HU1250 HITACHI H-1500 JEOL 2000EX JEOL 2010HT JEOL 2010UHR JEOL 2010F JEOL 3010HT JEOL 3010UHR JEOL KYOTO-3000SFF JEOL 4000EX JEOL HAREM JEOL ARM-1000 JEOL KYOTO-1000 JEOL ARM-1250 FEI/PHILIPS CM120T FEI/PHILIPS CM200T FEI/PHILIPS CM20/ST FEI/PHILIPS CM20/SOPHIE FEI/PHILIPS CM200FEG/ST FEI/PHILIPS CM20/UT FEI/PHILIPS CM200FEG/UT FEI/PHILIPS CM30/T FEI/PHILIPS CM300FEG/T FEI/PHILIPS CM300FEG/HE FEI/PHILIPS CM30/ST FEI/PHILIPS CM300FEG/ST FEI/PHILIPS CM300FEG/UT FEI TECNAI 12 FEI TECNAI 20 FEI TECNAI F20 FEI TECNAI F30 FEI MORGAGNI The mode of imaging. BRIGHT FIELD DARK FIELD DIFFRACTION OTHER The spherical aberration coefficient (Cs) in millimetres, 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 <RCSB:em_sample_preparationCategory> <RCSB:em_sample_preparation entry_id="1DYL" id="1"> <RCSB:ph>7.6</RCSB:ph> <RCSB:buffer_id>1</RCSB:buffer_id> <RCSB:sample_concentration>5.</RCSB:sample_concentration> </RCSB:em_sample_preparation> </RCSB: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 <RCSB:em_sample_supportCategory> <RCSB:em_sample_support id="1"> <RCSB:film_material>HOLEY CARBON</RCSB:film_material> <RCSB:grid_material>COPPER</RCSB:grid_material> <RCSB:grid_mesh_size>400</RCSB:grid_mesh_size> <RCSB:grid_type>MESH</RCSB:grid_type> <RCSB:pretreatment>GLOW DISCHARGE</RCSB:pretreatment> <RCSB:citation_id>2</RCSB:citation_id> </RCSB:em_sample_support> </RCSB: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 <RCSB:em_virus_entityCategory> <RCSB:em_virus_entity id="1" entity_assembly_id="1"> <RCSB:virus_host_category>VERTERBRATES</RCSB:virus_host_category> <RCSB:virus_host_species>HOMO SAPIENS</RCSB:virus_host_species> <RCSB:virus_type>VIRUS</RCSB:virus_type> <RCSB:virus_isolate>STRAIN</RCSB:virus_isolate> <RCSB:ictvdb_id>00.073.0.01.023</RCSB:ictvdb_id> <RCSB:enveloped>YES</RCSB:enveloped> <RCSB:empty>NO</RCSB:empty> </RCSB:em_virus_entity> </RCSB:em_virus_entityCategory> Additional details about this virus entity 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. ALGAE ARCHAEA BACTERIA(EUBACTERIA) FUNGI INVERTEBRATES PLANTAE (HIGHER PLANTS) PROTOZOA VERTEBRATES 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. VIRION SATELLITE PRION VIROID VIRUS-LIKE PARTICLE 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 <RCSB:em_vitrificationCategory> <RCSB:em_vitrification entry_id="1DYL" id="1"> <RCSB:sample_preparation_id>1</RCSB:sample_preparation_id> <RCSB:cryogen_name>ETHANE</RCSB:cryogen_name> <RCSB:humidity>90</RCSB:humidity> <RCSB:temp>95.</RCSB:temp> <RCSB:method>PLUNGE VITRIFICATION</RCSB:method> <RCSB:citation_id>1</RCSB:citation_id> <RCSB: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. </RCSB:details> </RCSB:em_vitrification> </RCSB: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 <RCSB:entityCategory> <RCSB:entity id="1"> <RCSB:type>polymer</RCSB:type> <RCSB:formula_weight>10916.</RCSB:formula_weight> <RCSB:details> The enzymatically competent form of HIV protease is a dimer. This entity corresponds to one monomer of an active dimer.</RCSB:details> </RCSB:entity> <RCSB:entity id="2"> <RCSB:type>non-polymer</RCSB:type> <RCSB:formula_weight>762.</RCSB:formula_weight> </RCSB:entity> <RCSB:entity id="3"> <RCSB:type>water</RCSB:type> <RCSB:formula_weight>18.</RCSB:formula_weight> </RCSB:entity> </RCSB:entityCategory> Number of entity molecules in the biological assembly. 1 2 3 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. DNA (5'-D(*GP*(CH3)CP*GP*(CH3)CP*GP*C)-3') PROFLAVINE PROTEIN (DEOXYRIBONUCLEASE I (E.C.3.1.21.1)) 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. 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 <RCSB:entity_keywordsCategory> <RCSB:entity_keywords entity_id="1"> <RCSB:text>polypeptide</RCSB:text> </RCSB:entity_keywords> <RCSB:entity_keywords entity_id="2"> <RCSB:text>natural product</RCSB:text> </RCSB:entity_keywords> <RCSB:entity_keywords entity_id="2"> <RCSB:text>inhibitor</RCSB:text> </RCSB:entity_keywords> <RCSB:entity_keywords entity_id="2"> <RCSB:text>reduced peptide</RCSB:text> </RCSB:entity_keywords> </RCSB:entity_keywordsCategory> PDB placeholder. Enzyme Comission number 2.7.7.7 Entity fragment description. KLENOW FRAGMENT REPLICASE OPERATOR HAIRPIN C-TERMINAL DOMAIN Details about an entity mutation. C280S 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 <RCSB:entity_name_comCategory> <RCSB:entity_name_com entity_id="1" name="HIV-1 protease monomer"></RCSB:entity_name_com> <RCSB:entity_name_com entity_id="1" name="HIV-1 PR monomer"></RCSB:entity_name_com> <RCSB:entity_name_com entity_id="2" name="acetyl-pepstatin"></RCSB:entity_name_com> <RCSB:entity_name_com entity_id="2" name="acetyl-Ile-Val-Asp-Statine-Ala-Ile-Statine"></RCSB:entity_name_com> <RCSB:entity_name_com entity_id="3" name="water"></RCSB:entity_name_com> </RCSB: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 <RCSB:entity_name_sysCategory> <RCSB:entity_name_sys entity_id="1" name="ECx.x.x.x"></RCSB:entity_name_sys> <RCSB:entity_name_sys entity_id="2" name="acetyl-Ile-Val-Asp-Sta-Ala-Ile-Sta"></RCSB:entity_name_sys> <RCSB:entity_name_sys entity_id="3" name="H(2)0"></RCSB:entity_name_sys> </RCSB: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 <RCSB:entity_polyCategory> <RCSB:entity_poly entity_id="1"> <RCSB:type>polypeptide(L)</RCSB:type> <RCSB:nstd_chirality>no</RCSB:nstd_chirality> <RCSB:nstd_linkage>no</RCSB:nstd_linkage> <RCSB:nstd_monomer>no</RCSB:nstd_monomer> </RCSB:entity_poly> </RCSB:entity_polyCategory> The chain_id(s) corresponding to this polymer entity. A B C D Chemical sequence expressed as string of one-letter amino acid codes including modifications. 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 X for modified or unknown MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGAAFNVEFD 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 Chemical sequence expressed as string of three-letter amino acid codes. 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 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. The sequence's target identifier registered at target database. 356560 C-terminal cloning artifacts and/or HIS tag. HHHHHH N-terminal cloning artifacts and/or HIS tag. HHHHHH The sequence position in the database sequence at which the alignment with your sequence begins. 59 The sequence position in the database sequence at which the alignment with your sequence ends. 685 The identifier for this sequence in the sequence data base. P00730 The name of the sequence data base containing a database entry for this sequence. Enter UNP for a Uniport entry Enter SWS for a Swiss-Prot entry Enter GB for a GenBank entry Enter EMBL for an European Molecular Biology Laboratory entry Enter PIR for a Protein Information Resource entry 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 <RCSB:entity_poly_seqCategory> <RCSB:entity_poly_seq entity_id="1" num="1" mon_id="PRO"></RCSB:entity_poly_seq> <RCSB:entity_poly_seq entity_id="1" num="2" mon_id="GLN"></RCSB:entity_poly_seq> <RCSB:entity_poly_seq entity_id="1" num="3" mon_id="ILE"></RCSB:entity_poly_seq> <RCSB:entity_poly_seq entity_id="1" num="4" mon_id="THR"></RCSB:entity_poly_seq> <RCSB:entity_poly_seq entity_id="1" num="5" mon_id="LEU"></RCSB:entity_poly_seq> <RCSB:entity_poly_seq entity_id="1" num="6" mon_id="TRP"></RCSB:entity_poly_seq> <RCSB:entity_poly_seq entity_id="1" num="7" mon_id="GLN"></RCSB:entity_poly_seq> <RCSB:entity_poly_seq entity_id="1" num="8" mon_id="ARG"></RCSB:entity_poly_seq> <RCSB:entity_poly_seq entity_id="1" num="9" mon_id="PRO"></RCSB:entity_poly_seq> <RCSB:entity_poly_seq entity_id="1" num="10" mon_id="LEU"></RCSB:entity_poly_seq> <RCSB:entity_poly_seq entity_id="1" num="11" mon_id="VAL"></RCSB:entity_poly_seq> <RCSB:entity_poly_seq entity_id="1" num="12" mon_id="THR"></RCSB:entity_poly_seq> <RCSB:entity_poly_seq entity_id="1" num="13" mon_id="ILE"></RCSB:entity_poly_seq> <RCSB:entity_poly_seq entity_id="1" num="14" mon_id="LYS"></RCSB:entity_poly_seq> <RCSB:entity_poly_seq entity_id="1" num="15" mon_id="ILE"></RCSB:entity_poly_seq> <RCSB:entity_poly_seq entity_id="1" num="16" mon_id="GLY"></RCSB:entity_poly_seq> <RCSB:entity_poly_seq entity_id="1" num="17" mon_id="GLY"></RCSB:entity_poly_seq> <RCSB:entity_poly_seq entity_id="1" num="18" mon_id="GLN"></RCSB:entity_poly_seq> <RCSB:entity_poly_seq entity_id="1" num="19" mon_id="LEU"></RCSB:entity_poly_seq> <RCSB:entity_poly_seq entity_id="1" num="20" mon_id="LYS"></RCSB:entity_poly_seq> <RCSB:entity_poly_seq entity_id="1" num="21" mon_id="GLU"></RCSB:entity_poly_seq> <RCSB:entity_poly_seq entity_id="1" num="22" mon_id="ALA"></RCSB:entity_poly_seq> <RCSB:entity_poly_seq entity_id="1" num="23" mon_id="LEU"></RCSB:entity_poly_seq> <RCSB:entity_poly_seq entity_id="1" num="24" mon_id="LEU"></RCSB:entity_poly_seq> <RCSB:entity_poly_seq entity_id="1" num="25" mon_id="ASP"></RCSB:entity_poly_seq> </RCSB: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 <RCSB:entity_src_genCategory> <RCSB:entity_src_gen entity_id="1"> <RCSB:gene_src_common_name>HIV-1</RCSB:gene_src_common_name> <RCSB:gene_src_strain>NY-5</RCSB:gene_src_strain> <RCSB:host_org_common_name>bacteria</RCSB:host_org_common_name> <RCSB:host_org_genus>Escherichia</RCSB:host_org_genus> <RCSB:host_org_species>coli</RCSB:host_org_species> <RCSB:plasmid_name>pB322</RCSB:plasmid_name> </RCSB:entity_src_gen> </RCSB:entity_src_genCategory> 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. 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 Culture collection identifier. 6051 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 Spodoptera frugiperda Cricetulus griseus 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 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 <RCSB:entity_src_natCategory> <RCSB:entity_src_nat entity_id="2"> <RCSB:common_name>bacteria</RCSB:common_name> <RCSB:genus>Actinomycetes</RCSB:genus> <RCSB:species xsi:nil="true" /> <RCSB: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.</RCSB:details> </RCSB:entity_src_nat> </RCSB: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. Culture Collection identifier. 6051 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 <RCSB:entryCategory> <RCSB:entry id="5HVP"></RCSB:entry> </RCSB:entryCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. <RCSB:entryCategory> <RCSB:entry id="TOZ"></RCSB:entry> </RCSB: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~. <RCSB:entry_linkCategory> <RCSB:entry_link id="KSE_COM" entry_id="KSE_TEXT"> <RCSB:details>experimental data common to ref./mod. structures</RCSB:details> </RCSB:entry_link> <RCSB:entry_link id="KSE_REF" entry_id="KSE_TEXT"> <RCSB:details>reference structure</RCSB:details> </RCSB:entry_link> <RCSB:entry_link id="KSE_MOD" entry_id="KSE_TEXT"> <RCSB:details>modulated structure</RCSB:details> </RCSB:entry_link> </RCSB: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 <RCSB:exptlCategory> <RCSB:exptl entry_id="datablock1"> <RCSB:absorpt_coefficient_mu>1.22</RCSB:absorpt_coefficient_mu> <RCSB:absorpt_correction_T_max>0.896</RCSB:absorpt_correction_T_max> <RCSB:absorpt_correction_T_min>0.802</RCSB:absorpt_correction_T_min> <RCSB:absorpt_correction_type>integration</RCSB:absorpt_correction_type> <RCSB:absorpt_process_details> Gaussian grid method from SHELX76 Sheldrick, G. M., &quot;SHELX-76: structure determination and refinement program&quot;, Cambridge University, UK, 1976</RCSB:absorpt_process_details> <RCSB:crystals_number>1</RCSB:crystals_number> <RCSB:details> Enraf-Nonius LT2 liquid nitrogen variable-temperature device used</RCSB:details> <RCSB:method>single-crystal x-ray diffraction</RCSB:method> <RCSB:method_details> graphite monochromatized Cu K(alpha) fixed tube and Enraf-Nonius CAD4 diffractometer used</RCSB:method_details> </RCSB:exptl> </RCSB: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 <RCSB:exptl_crystalCategory> <RCSB:exptl_crystal id="xst2l"> <RCSB:colour>pale yellow</RCSB:colour> <RCSB:density_diffrn>1.113</RCSB:density_diffrn> <RCSB:density_Matthews>1.01</RCSB:density_Matthews> <RCSB:density_meas>1.11</RCSB:density_meas> <RCSB:density_meas_temp>294.5</RCSB:density_meas_temp> <RCSB:density_method>neutral buoyancy</RCSB:density_method> <RCSB:density_percent_sol>0.15</RCSB:density_percent_sol> <RCSB:description>hexagonal rod, uncut</RCSB:description> <RCSB:F_000>202</RCSB:F_000> <RCSB:preparation> hanging drop, crystal soaked in 10&#37; ethylene glycol for 10 h, then placed in nylon loop at data collection time</RCSB:preparation> <RCSB:size_max>0.30</RCSB:size_max> <RCSB:size_mid>0.20</RCSB:size_mid> <RCSB:size_min>0.05</RCSB:size_min> <RCSB:size_rad>0.025</RCSB:size_rad> </RCSB:exptl_crystal> </RCSB: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 measured diffraction limit for this crystal. The measured diffraction limit for this crystal. The crystal size along the first measured direction in millimeters. The crystal size along the second measured direction in millimeters. The crystal size along the third measured direction in millimeters. A code to indicate that a crystal image is available for this crystal. A code to indicate that an x-ray image is available for this crystal. A description of the type of x-ray image for this crystal. 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). 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 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. 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. <RCSB:exptl_crystal_faceCategory> <RCSB:exptl_crystal_face crystal_id="xstl1" index_h="1" index_k="0" index_l="0"> <RCSB:diffr_chi>42.56</RCSB:diffr_chi> <RCSB:diffr_kappa>30.23</RCSB:diffr_kappa> <RCSB:diffr_phi>-125.56</RCSB:diffr_phi> <RCSB:diffr_psi>-0.34</RCSB:diffr_psi> <RCSB:perp_dist>0.025</RCSB:perp_dist> </RCSB:exptl_crystal_face> </RCSB: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 <RCSB:exptl_crystal_growCategory> <RCSB:exptl_crystal_grow crystal_id="1"> <RCSB:method>hanging drop</RCSB:method> <RCSB:apparatus>Linbro plates</RCSB:apparatus> <RCSB:atmosphere>room air</RCSB:atmosphere> <RCSB:pH>4.7</RCSB:pH> <RCSB:temp>18(3).</RCSB:temp> <RCSB:time>approximately 2 days</RCSB:time> </RCSB:exptl_crystal_grow> </RCSB: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 The ambient pressure in kilopascals at which the crystal was grown. The estimated standard deviation of attribute pressure in category exptl_crystal_grow. The range of pH values at which the crystal was grown. Used when a point estimate of pH is not appropriate. 5.5 - 6.3 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 <RCSB:exptl_crystal_grow_compCategory> <RCSB:exptl_crystal_grow_comp crystal_id="1" id="1"> <RCSB:sol_id>1</RCSB:sol_id> <RCSB:name>HIV-1 protease</RCSB:name> <RCSB:volume>0.002 ml</RCSB:volume> <RCSB:conc>6 mg/ml</RCSB:conc> <RCSB:details> The protein solution was in a buffer containing 25 mM NaCl, 100 mM NaMES/ MES buffer, pH 7.5, 3 mM NaAzide</RCSB:details> </RCSB:exptl_crystal_grow_comp> <RCSB:exptl_crystal_grow_comp crystal_id="1" id="2"> <RCSB:sol_id>2</RCSB:sol_id> <RCSB:name>NaCl</RCSB:name> <RCSB:volume>0.200 ml</RCSB:volume> <RCSB:conc>4 M</RCSB:conc> <RCSB:details>in 3 mM NaAzide</RCSB:details> </RCSB:exptl_crystal_grow_comp> <RCSB:exptl_crystal_grow_comp crystal_id="1" id="3"> <RCSB:sol_id>2</RCSB:sol_id> <RCSB:name>Acetic Acid</RCSB:name> <RCSB:volume>0.047 ml</RCSB:volume> <RCSB:conc>100 mM</RCSB:conc> <RCSB:details>in 3 mM NaAzide</RCSB:details> </RCSB:exptl_crystal_grow_comp> <RCSB:exptl_crystal_grow_comp crystal_id="1" id="4"> <RCSB:sol_id>2</RCSB:sol_id> <RCSB:name>Na Acetate</RCSB:name> <RCSB:volume>0.053 ml</RCSB:volume> <RCSB:conc>100 mM</RCSB:conc> <RCSB: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.</RCSB:details> </RCSB:exptl_crystal_grow_comp> <RCSB:exptl_crystal_grow_comp crystal_id="1" id="5"> <RCSB:sol_id>2</RCSB:sol_id> <RCSB:name>water</RCSB:name> <RCSB:volume>0.700 ml</RCSB:volume> <RCSB:conc>neat</RCSB:conc> <RCSB:details>in 3 mM NaAzide</RCSB:details> </RCSB:exptl_crystal_grow_comp> </RCSB:exptl_crystal_grow_compCategory> The concentration of this component in the final crystallization solution. This data item should include units of concentration. 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 fr