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. The data items for describing anisotropic 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. <mmcif_mdb:atom_siteCategory> <mmcif_mdb:atom_site id="1"> <mmcif_mdb:B_iso_or_equiv>17.93</mmcif_mdb:B_iso_or_equiv> <mmcif_mdb:Cartn_x>25.369</mmcif_mdb:Cartn_x> <mmcif_mdb:Cartn_y>30.691</mmcif_mdb:Cartn_y> <mmcif_mdb:Cartn_z>11.795</mmcif_mdb:Cartn_z> <mmcif_mdb:auth_seq_id>11</mmcif_mdb:auth_seq_id> <mmcif_mdb:footnote_id></mmcif_mdb:footnote_id> <mmcif_mdb:group_PDB>ATOM</mmcif_mdb:group_PDB> <mmcif_mdb:label_alt_id></mmcif_mdb:label_alt_id> <mmcif_mdb:label_asym_id>A</mmcif_mdb:label_asym_id> <mmcif_mdb:label_atom_id>N</mmcif_mdb:label_atom_id> <mmcif_mdb:label_comp_id>VAL</mmcif_mdb:label_comp_id> <mmcif_mdb:label_seq_id>11</mmcif_mdb:label_seq_id> <mmcif_mdb:occupancy>1.00</mmcif_mdb:occupancy> <mmcif_mdb:type_symbol>N</mmcif_mdb:type_symbol> </mmcif_mdb:atom_site> <mmcif_mdb:atom_site id="2"> <mmcif_mdb:B_iso_or_equiv>17.75</mmcif_mdb:B_iso_or_equiv> <mmcif_mdb:Cartn_x>25.970</mmcif_mdb:Cartn_x> <mmcif_mdb:Cartn_y>31.965</mmcif_mdb:Cartn_y> <mmcif_mdb:Cartn_z>12.332</mmcif_mdb:Cartn_z> <mmcif_mdb:auth_seq_id>11</mmcif_mdb:auth_seq_id> <mmcif_mdb:footnote_id></mmcif_mdb:footnote_id> <mmcif_mdb:group_PDB>ATOM</mmcif_mdb:group_PDB> <mmcif_mdb:label_alt_id></mmcif_mdb:label_alt_id> <mmcif_mdb:label_asym_id>A</mmcif_mdb:label_asym_id> <mmcif_mdb:label_atom_id>CA</mmcif_mdb:label_atom_id> <mmcif_mdb:label_comp_id>VAL</mmcif_mdb:label_comp_id> <mmcif_mdb:label_seq_id>11</mmcif_mdb:label_seq_id> <mmcif_mdb:occupancy>1.00</mmcif_mdb:occupancy> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:atom_site> <mmcif_mdb:atom_site id="3"> <mmcif_mdb:B_iso_or_equiv>17.83</mmcif_mdb:B_iso_or_equiv> <mmcif_mdb:Cartn_x>25.569</mmcif_mdb:Cartn_x> <mmcif_mdb:Cartn_y>32.010</mmcif_mdb:Cartn_y> <mmcif_mdb:Cartn_z>13.808</mmcif_mdb:Cartn_z> <mmcif_mdb:auth_seq_id>11</mmcif_mdb:auth_seq_id> <mmcif_mdb:footnote_id></mmcif_mdb:footnote_id> <mmcif_mdb:group_PDB>ATOM</mmcif_mdb:group_PDB> <mmcif_mdb:label_alt_id></mmcif_mdb:label_alt_id> <mmcif_mdb:label_asym_id>A</mmcif_mdb:label_asym_id> <mmcif_mdb:label_atom_id>C</mmcif_mdb:label_atom_id> <mmcif_mdb:label_comp_id>VAL</mmcif_mdb:label_comp_id> <mmcif_mdb:label_seq_id>11</mmcif_mdb:label_seq_id> <mmcif_mdb:occupancy>1.00</mmcif_mdb:occupancy> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:atom_site> <mmcif_mdb:atom_site id="4"> <mmcif_mdb:B_iso_or_equiv>17.53</mmcif_mdb:B_iso_or_equiv> <mmcif_mdb:Cartn_x>24.735</mmcif_mdb:Cartn_x> <mmcif_mdb:Cartn_y>31.190</mmcif_mdb:Cartn_y> <mmcif_mdb:Cartn_z>14.167</mmcif_mdb:Cartn_z> <mmcif_mdb:auth_seq_id>11</mmcif_mdb:auth_seq_id> <mmcif_mdb:footnote_id></mmcif_mdb:footnote_id> <mmcif_mdb:group_PDB>ATOM</mmcif_mdb:group_PDB> <mmcif_mdb:label_alt_id></mmcif_mdb:label_alt_id> <mmcif_mdb:label_asym_id>A</mmcif_mdb:label_asym_id> <mmcif_mdb:label_atom_id>O</mmcif_mdb:label_atom_id> <mmcif_mdb:label_comp_id>VAL</mmcif_mdb:label_comp_id> <mmcif_mdb:label_seq_id>11</mmcif_mdb:label_seq_id> <mmcif_mdb:occupancy>1.00</mmcif_mdb:occupancy> <mmcif_mdb:type_symbol>O</mmcif_mdb:type_symbol> </mmcif_mdb:atom_site> <mmcif_mdb:atom_site id="5"> <mmcif_mdb:B_iso_or_equiv>17.66</mmcif_mdb:B_iso_or_equiv> <mmcif_mdb:Cartn_x>25.379</mmcif_mdb:Cartn_x> <mmcif_mdb:Cartn_y>33.146</mmcif_mdb:Cartn_y> <mmcif_mdb:Cartn_z>11.540</mmcif_mdb:Cartn_z> <mmcif_mdb:auth_seq_id>11</mmcif_mdb:auth_seq_id> <mmcif_mdb:footnote_id></mmcif_mdb:footnote_id> <mmcif_mdb:group_PDB>ATOM</mmcif_mdb:group_PDB> <mmcif_mdb:label_alt_id></mmcif_mdb:label_alt_id> <mmcif_mdb:label_asym_id>A</mmcif_mdb:label_asym_id> <mmcif_mdb:label_atom_id>CB</mmcif_mdb:label_atom_id> <mmcif_mdb:label_comp_id>VAL</mmcif_mdb:label_comp_id> <mmcif_mdb:label_seq_id>11</mmcif_mdb:label_seq_id> <mmcif_mdb:occupancy>1.00</mmcif_mdb:occupancy> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:atom_site> <mmcif_mdb:atom_site id="6"> <mmcif_mdb:B_iso_or_equiv>18.86</mmcif_mdb:B_iso_or_equiv> <mmcif_mdb:Cartn_x>25.584</mmcif_mdb:Cartn_x> <mmcif_mdb:Cartn_y>33.034</mmcif_mdb:Cartn_y> <mmcif_mdb:Cartn_z>10.030</mmcif_mdb:Cartn_z> <mmcif_mdb:auth_seq_id>11</mmcif_mdb:auth_seq_id> <mmcif_mdb:footnote_id></mmcif_mdb:footnote_id> <mmcif_mdb:group_PDB>ATOM</mmcif_mdb:group_PDB> <mmcif_mdb:label_alt_id></mmcif_mdb:label_alt_id> <mmcif_mdb:label_asym_id>A</mmcif_mdb:label_asym_id> <mmcif_mdb:label_atom_id>CG1</mmcif_mdb:label_atom_id> <mmcif_mdb:label_comp_id>VAL</mmcif_mdb:label_comp_id> <mmcif_mdb:label_seq_id>11</mmcif_mdb:label_seq_id> <mmcif_mdb:occupancy>1.00</mmcif_mdb:occupancy> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:atom_site> <mmcif_mdb:atom_site id="7"> <mmcif_mdb:B_iso_or_equiv>17.12</mmcif_mdb:B_iso_or_equiv> <mmcif_mdb:Cartn_x>23.933</mmcif_mdb:Cartn_x> <mmcif_mdb:Cartn_y>33.309</mmcif_mdb:Cartn_y> <mmcif_mdb:Cartn_z>11.872</mmcif_mdb:Cartn_z> <mmcif_mdb:auth_seq_id>11</mmcif_mdb:auth_seq_id> <mmcif_mdb:footnote_id></mmcif_mdb:footnote_id> <mmcif_mdb:group_PDB>ATOM</mmcif_mdb:group_PDB> <mmcif_mdb:label_alt_id></mmcif_mdb:label_alt_id> <mmcif_mdb:label_asym_id>A</mmcif_mdb:label_asym_id> <mmcif_mdb:label_atom_id>CG2</mmcif_mdb:label_atom_id> <mmcif_mdb:label_comp_id>VAL</mmcif_mdb:label_comp_id> <mmcif_mdb:label_seq_id>11</mmcif_mdb:label_seq_id> <mmcif_mdb:occupancy>1.00</mmcif_mdb:occupancy> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:atom_site> <mmcif_mdb:atom_site id="8"> <mmcif_mdb:B_iso_or_equiv>18.97</mmcif_mdb:B_iso_or_equiv> <mmcif_mdb:Cartn_x>26.095</mmcif_mdb:Cartn_x> <mmcif_mdb:Cartn_y>32.930</mmcif_mdb:Cartn_y> <mmcif_mdb:Cartn_z>14.590</mmcif_mdb:Cartn_z> <mmcif_mdb:auth_seq_id>12</mmcif_mdb:auth_seq_id> <mmcif_mdb:footnote_id>4</mmcif_mdb:footnote_id> <mmcif_mdb:group_PDB>ATOM</mmcif_mdb:group_PDB> <mmcif_mdb:label_alt_id></mmcif_mdb:label_alt_id> <mmcif_mdb:label_asym_id>A</mmcif_mdb:label_asym_id> <mmcif_mdb:label_atom_id>N</mmcif_mdb:label_atom_id> <mmcif_mdb:label_comp_id>THR</mmcif_mdb:label_comp_id> <mmcif_mdb:label_seq_id>12</mmcif_mdb:label_seq_id> <mmcif_mdb:occupancy>1.00</mmcif_mdb:occupancy> <mmcif_mdb:type_symbol>N</mmcif_mdb:type_symbol> </mmcif_mdb:atom_site> <mmcif_mdb:atom_site id="9"> <mmcif_mdb:B_iso_or_equiv>19.80</mmcif_mdb:B_iso_or_equiv> <mmcif_mdb:Cartn_x>25.734</mmcif_mdb:Cartn_x> <mmcif_mdb:Cartn_y>32.995</mmcif_mdb:Cartn_y> <mmcif_mdb:Cartn_z>16.032</mmcif_mdb:Cartn_z> <mmcif_mdb:auth_seq_id>12</mmcif_mdb:auth_seq_id> <mmcif_mdb:footnote_id>4</mmcif_mdb:footnote_id> <mmcif_mdb:group_PDB>ATOM</mmcif_mdb:group_PDB> <mmcif_mdb:label_alt_id></mmcif_mdb:label_alt_id> <mmcif_mdb:label_asym_id>A</mmcif_mdb:label_asym_id> <mmcif_mdb:label_atom_id>CA</mmcif_mdb:label_atom_id> <mmcif_mdb:label_comp_id>THR</mmcif_mdb:label_comp_id> <mmcif_mdb:label_seq_id>12</mmcif_mdb:label_seq_id> <mmcif_mdb:occupancy>1.00</mmcif_mdb:occupancy> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:atom_site> <mmcif_mdb:atom_site id="10"> <mmcif_mdb:B_iso_or_equiv>20.92</mmcif_mdb:B_iso_or_equiv> <mmcif_mdb:Cartn_x>24.695</mmcif_mdb:Cartn_x> <mmcif_mdb:Cartn_y>34.106</mmcif_mdb:Cartn_y> <mmcif_mdb:Cartn_z>16.113</mmcif_mdb:Cartn_z> <mmcif_mdb:auth_seq_id>12</mmcif_mdb:auth_seq_id> <mmcif_mdb:footnote_id>4</mmcif_mdb:footnote_id> <mmcif_mdb:group_PDB>ATOM</mmcif_mdb:group_PDB> <mmcif_mdb:label_alt_id></mmcif_mdb:label_alt_id> <mmcif_mdb:label_asym_id>A</mmcif_mdb:label_asym_id> <mmcif_mdb:label_atom_id>C</mmcif_mdb:label_atom_id> <mmcif_mdb:label_comp_id>THR</mmcif_mdb:label_comp_id> <mmcif_mdb:label_seq_id>12</mmcif_mdb:label_seq_id> <mmcif_mdb:occupancy>1.00</mmcif_mdb:occupancy> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:atom_site> <mmcif_mdb:atom_site id="11"> <mmcif_mdb:B_iso_or_equiv>21.84</mmcif_mdb:B_iso_or_equiv> <mmcif_mdb:Cartn_x>24.869</mmcif_mdb:Cartn_x> <mmcif_mdb:Cartn_y>35.118</mmcif_mdb:Cartn_y> <mmcif_mdb:Cartn_z>15.421</mmcif_mdb:Cartn_z> <mmcif_mdb:auth_seq_id>12</mmcif_mdb:auth_seq_id> <mmcif_mdb:footnote_id>4</mmcif_mdb:footnote_id> <mmcif_mdb:group_PDB>ATOM</mmcif_mdb:group_PDB> <mmcif_mdb:label_alt_id></mmcif_mdb:label_alt_id> <mmcif_mdb:label_asym_id>A</mmcif_mdb:label_asym_id> <mmcif_mdb:label_atom_id>O</mmcif_mdb:label_atom_id> <mmcif_mdb:label_comp_id>THR</mmcif_mdb:label_comp_id> <mmcif_mdb:label_seq_id>12</mmcif_mdb:label_seq_id> <mmcif_mdb:occupancy>1.00</mmcif_mdb:occupancy> <mmcif_mdb:type_symbol>O</mmcif_mdb:type_symbol> </mmcif_mdb:atom_site> <mmcif_mdb:atom_site id="12"> <mmcif_mdb:B_iso_or_equiv>20.51</mmcif_mdb:B_iso_or_equiv> <mmcif_mdb:Cartn_x>26.911</mmcif_mdb:Cartn_x> <mmcif_mdb:Cartn_y>33.346</mmcif_mdb:Cartn_y> <mmcif_mdb:Cartn_z>17.018</mmcif_mdb:Cartn_z> <mmcif_mdb:auth_seq_id>12</mmcif_mdb:auth_seq_id> <mmcif_mdb:footnote_id>4</mmcif_mdb:footnote_id> <mmcif_mdb:group_PDB>ATOM</mmcif_mdb:group_PDB> <mmcif_mdb:label_alt_id></mmcif_mdb:label_alt_id> <mmcif_mdb:label_asym_id>A</mmcif_mdb:label_asym_id> <mmcif_mdb:label_atom_id>CB</mmcif_mdb:label_atom_id> <mmcif_mdb:label_comp_id>THR</mmcif_mdb:label_comp_id> <mmcif_mdb:label_seq_id>12</mmcif_mdb:label_seq_id> <mmcif_mdb:occupancy>1.00</mmcif_mdb:occupancy> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:atom_site> <mmcif_mdb:atom_site id="13"> <mmcif_mdb:B_iso_or_equiv>20.29</mmcif_mdb:B_iso_or_equiv> <mmcif_mdb:Cartn_x>27.946</mmcif_mdb:Cartn_x> <mmcif_mdb:Cartn_y>33.921</mmcif_mdb:Cartn_y> <mmcif_mdb:Cartn_z>16.183</mmcif_mdb:Cartn_z> <mmcif_mdb:auth_seq_id>12</mmcif_mdb:auth_seq_id> <mmcif_mdb:footnote_id>4</mmcif_mdb:footnote_id> <mmcif_mdb:group_PDB>ATOM</mmcif_mdb:group_PDB> <mmcif_mdb:label_alt_id>3</mmcif_mdb:label_alt_id> <mmcif_mdb:label_asym_id>A</mmcif_mdb:label_asym_id> <mmcif_mdb:label_atom_id>OG1</mmcif_mdb:label_atom_id> <mmcif_mdb:label_comp_id>THR</mmcif_mdb:label_comp_id> <mmcif_mdb:label_seq_id>12</mmcif_mdb:label_seq_id> <mmcif_mdb:occupancy>0.50</mmcif_mdb:occupancy> <mmcif_mdb:type_symbol>O</mmcif_mdb:type_symbol> </mmcif_mdb:atom_site> <mmcif_mdb:atom_site id="14"> <mmcif_mdb:B_iso_or_equiv>20.59</mmcif_mdb:B_iso_or_equiv> <mmcif_mdb:Cartn_x>27.769</mmcif_mdb:Cartn_x> <mmcif_mdb:Cartn_y>32.142</mmcif_mdb:Cartn_y> <mmcif_mdb:Cartn_z>17.103</mmcif_mdb:Cartn_z> <mmcif_mdb:auth_seq_id>12</mmcif_mdb:auth_seq_id> <mmcif_mdb:footnote_id>4</mmcif_mdb:footnote_id> <mmcif_mdb:group_PDB>ATOM</mmcif_mdb:group_PDB> <mmcif_mdb:label_alt_id>4</mmcif_mdb:label_alt_id> <mmcif_mdb:label_asym_id>A</mmcif_mdb:label_asym_id> <mmcif_mdb:label_atom_id>OG1</mmcif_mdb:label_atom_id> <mmcif_mdb:label_comp_id>THR</mmcif_mdb:label_comp_id> <mmcif_mdb:label_seq_id>12</mmcif_mdb:label_seq_id> <mmcif_mdb:occupancy>0.50</mmcif_mdb:occupancy> <mmcif_mdb:type_symbol>O</mmcif_mdb:type_symbol> </mmcif_mdb:atom_site> <mmcif_mdb:atom_site id="15"> <mmcif_mdb:B_iso_or_equiv>20.47</mmcif_mdb:B_iso_or_equiv> <mmcif_mdb:Cartn_x>27.418</mmcif_mdb:Cartn_x> <mmcif_mdb:Cartn_y>32.181</mmcif_mdb:Cartn_y> <mmcif_mdb:Cartn_z>17.878</mmcif_mdb:Cartn_z> <mmcif_mdb:auth_seq_id>12</mmcif_mdb:auth_seq_id> <mmcif_mdb:footnote_id>4</mmcif_mdb:footnote_id> <mmcif_mdb:group_PDB>ATOM</mmcif_mdb:group_PDB> <mmcif_mdb:label_alt_id>3</mmcif_mdb:label_alt_id> <mmcif_mdb:label_asym_id>A</mmcif_mdb:label_asym_id> <mmcif_mdb:label_atom_id>CG2</mmcif_mdb:label_atom_id> <mmcif_mdb:label_comp_id>THR</mmcif_mdb:label_comp_id> <mmcif_mdb:label_seq_id>12</mmcif_mdb:label_seq_id> <mmcif_mdb:occupancy>0.50</mmcif_mdb:occupancy> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:atom_site> <mmcif_mdb:atom_site id="16"> <mmcif_mdb:B_iso_or_equiv>20.00</mmcif_mdb:B_iso_or_equiv> <mmcif_mdb:Cartn_x>26.489</mmcif_mdb:Cartn_x> <mmcif_mdb:Cartn_y>33.778</mmcif_mdb:Cartn_y> <mmcif_mdb:Cartn_z>18.426</mmcif_mdb:Cartn_z> <mmcif_mdb:auth_seq_id>12</mmcif_mdb:auth_seq_id> <mmcif_mdb:footnote_id>4</mmcif_mdb:footnote_id> <mmcif_mdb:group_PDB>ATOM</mmcif_mdb:group_PDB> <mmcif_mdb:label_alt_id>4</mmcif_mdb:label_alt_id> <mmcif_mdb:label_asym_id>A</mmcif_mdb:label_asym_id> <mmcif_mdb:label_atom_id>CG2</mmcif_mdb:label_atom_id> <mmcif_mdb:label_comp_id>THR</mmcif_mdb:label_comp_id> <mmcif_mdb:label_seq_id>12</mmcif_mdb:label_seq_id> <mmcif_mdb:occupancy>0.50</mmcif_mdb:occupancy> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:atom_site> <mmcif_mdb:atom_site id="17"> <mmcif_mdb:B_iso_or_equiv>22.08</mmcif_mdb:B_iso_or_equiv> <mmcif_mdb:Cartn_x>23.664</mmcif_mdb:Cartn_x> <mmcif_mdb:Cartn_y>33.855</mmcif_mdb:Cartn_y> <mmcif_mdb:Cartn_z>16.884</mmcif_mdb:Cartn_z> <mmcif_mdb:auth_seq_id>13</mmcif_mdb:auth_seq_id> <mmcif_mdb:footnote_id></mmcif_mdb:footnote_id> <mmcif_mdb:group_PDB>ATOM</mmcif_mdb:group_PDB> <mmcif_mdb:label_alt_id></mmcif_mdb:label_alt_id> <mmcif_mdb:label_asym_id>A</mmcif_mdb:label_asym_id> <mmcif_mdb:label_atom_id>N</mmcif_mdb:label_atom_id> <mmcif_mdb:label_comp_id>ILE</mmcif_mdb:label_comp_id> <mmcif_mdb:label_seq_id>13</mmcif_mdb:label_seq_id> <mmcif_mdb:occupancy>1.00</mmcif_mdb:occupancy> <mmcif_mdb:type_symbol>N</mmcif_mdb:type_symbol> </mmcif_mdb:atom_site> <mmcif_mdb:atom_site id="18"> <mmcif_mdb:B_iso_or_equiv>23.44</mmcif_mdb:B_iso_or_equiv> <mmcif_mdb:Cartn_x>22.623</mmcif_mdb:Cartn_x> <mmcif_mdb:Cartn_y>34.850</mmcif_mdb:Cartn_y> <mmcif_mdb:Cartn_z>17.093</mmcif_mdb:Cartn_z> <mmcif_mdb:auth_seq_id>13</mmcif_mdb:auth_seq_id> <mmcif_mdb:footnote_id></mmcif_mdb:footnote_id> <mmcif_mdb:group_PDB>ATOM</mmcif_mdb:group_PDB> <mmcif_mdb:label_alt_id></mmcif_mdb:label_alt_id> <mmcif_mdb:label_asym_id>A</mmcif_mdb:label_asym_id> <mmcif_mdb:label_atom_id>CA</mmcif_mdb:label_atom_id> <mmcif_mdb:label_comp_id>ILE</mmcif_mdb:label_comp_id> <mmcif_mdb:label_seq_id>13</mmcif_mdb:label_seq_id> <mmcif_mdb:occupancy>1.00</mmcif_mdb:occupancy> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:atom_site> <mmcif_mdb:atom_site id="19"> <mmcif_mdb:B_iso_or_equiv>25.77</mmcif_mdb:B_iso_or_equiv> <mmcif_mdb:Cartn_x>22.657</mmcif_mdb:Cartn_x> <mmcif_mdb:Cartn_y>35.113</mmcif_mdb:Cartn_y> <mmcif_mdb:Cartn_z>18.610</mmcif_mdb:Cartn_z> <mmcif_mdb:auth_seq_id>13</mmcif_mdb:auth_seq_id> <mmcif_mdb:footnote_id></mmcif_mdb:footnote_id> <mmcif_mdb:group_PDB>ATOM</mmcif_mdb:group_PDB> <mmcif_mdb:label_alt_id></mmcif_mdb:label_alt_id> <mmcif_mdb:label_asym_id>A</mmcif_mdb:label_asym_id> <mmcif_mdb:label_atom_id>C</mmcif_mdb:label_atom_id> <mmcif_mdb:label_comp_id>ILE</mmcif_mdb:label_comp_id> <mmcif_mdb:label_seq_id>13</mmcif_mdb:label_seq_id> <mmcif_mdb:occupancy>1.00</mmcif_mdb:occupancy> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:atom_site> <mmcif_mdb:atom_site id="20"> <mmcif_mdb:B_iso_or_equiv>26.28</mmcif_mdb:B_iso_or_equiv> <mmcif_mdb:Cartn_x>23.123</mmcif_mdb:Cartn_x> <mmcif_mdb:Cartn_y>34.250</mmcif_mdb:Cartn_y> <mmcif_mdb:Cartn_z>19.406</mmcif_mdb:Cartn_z> <mmcif_mdb:auth_seq_id>13</mmcif_mdb:auth_seq_id> <mmcif_mdb:footnote_id></mmcif_mdb:footnote_id> <mmcif_mdb:group_PDB>ATOM</mmcif_mdb:group_PDB> <mmcif_mdb:label_alt_id></mmcif_mdb:label_alt_id> <mmcif_mdb:label_asym_id>A</mmcif_mdb:label_asym_id> <mmcif_mdb:label_atom_id>O</mmcif_mdb:label_atom_id> <mmcif_mdb:label_comp_id>ILE</mmcif_mdb:label_comp_id> <mmcif_mdb:label_seq_id>13</mmcif_mdb:label_seq_id> <mmcif_mdb:occupancy>1.00</mmcif_mdb:occupancy> <mmcif_mdb:type_symbol>O</mmcif_mdb:type_symbol> </mmcif_mdb:atom_site> <mmcif_mdb:atom_site id="21"> <mmcif_mdb:B_iso_or_equiv>22.67</mmcif_mdb:B_iso_or_equiv> <mmcif_mdb:Cartn_x>21.236</mmcif_mdb:Cartn_x> <mmcif_mdb:Cartn_y>34.463</mmcif_mdb:Cartn_y> <mmcif_mdb:Cartn_z>16.492</mmcif_mdb:Cartn_z> <mmcif_mdb:auth_seq_id>13</mmcif_mdb:auth_seq_id> <mmcif_mdb:footnote_id></mmcif_mdb:footnote_id> <mmcif_mdb:group_PDB>ATOM</mmcif_mdb:group_PDB> <mmcif_mdb:label_alt_id></mmcif_mdb:label_alt_id> <mmcif_mdb:label_asym_id>A</mmcif_mdb:label_asym_id> <mmcif_mdb:label_atom_id>CB</mmcif_mdb:label_atom_id> <mmcif_mdb:label_comp_id>ILE</mmcif_mdb:label_comp_id> <mmcif_mdb:label_seq_id>13</mmcif_mdb:label_seq_id> <mmcif_mdb:occupancy>1.00</mmcif_mdb:occupancy> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:atom_site> <mmcif_mdb:atom_site id="22"> <mmcif_mdb:B_iso_or_equiv>22.14</mmcif_mdb:B_iso_or_equiv> <mmcif_mdb:Cartn_x>20.478</mmcif_mdb:Cartn_x> <mmcif_mdb:Cartn_y>33.469</mmcif_mdb:Cartn_y> <mmcif_mdb:Cartn_z>17.371</mmcif_mdb:Cartn_z> <mmcif_mdb:auth_seq_id>13</mmcif_mdb:auth_seq_id> <mmcif_mdb:footnote_id></mmcif_mdb:footnote_id> <mmcif_mdb:group_PDB>ATOM</mmcif_mdb:group_PDB> <mmcif_mdb:label_alt_id></mmcif_mdb:label_alt_id> <mmcif_mdb:label_asym_id>A</mmcif_mdb:label_asym_id> <mmcif_mdb:label_atom_id>CG1</mmcif_mdb:label_atom_id> <mmcif_mdb:label_comp_id>ILE</mmcif_mdb:label_comp_id> <mmcif_mdb:label_seq_id>13</mmcif_mdb:label_seq_id> <mmcif_mdb:occupancy>1.00</mmcif_mdb:occupancy> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:atom_site> <mmcif_mdb:atom_site id="23"> <mmcif_mdb:B_iso_or_equiv>21.75</mmcif_mdb:B_iso_or_equiv> <mmcif_mdb:Cartn_x>21.357</mmcif_mdb:Cartn_x> <mmcif_mdb:Cartn_y>33.986</mmcif_mdb:Cartn_y> <mmcif_mdb:Cartn_z>15.016</mmcif_mdb:Cartn_z> <mmcif_mdb:auth_seq_id>13</mmcif_mdb:auth_seq_id> <mmcif_mdb:footnote_id></mmcif_mdb:footnote_id> <mmcif_mdb:group_PDB>ATOM</mmcif_mdb:group_PDB> <mmcif_mdb:label_alt_id></mmcif_mdb:label_alt_id> <mmcif_mdb:label_asym_id>A</mmcif_mdb:label_asym_id> <mmcif_mdb:label_atom_id>CG2</mmcif_mdb:label_atom_id> <mmcif_mdb:label_comp_id>ILE</mmcif_mdb:label_comp_id> <mmcif_mdb:label_seq_id>13</mmcif_mdb:label_seq_id> <mmcif_mdb:occupancy>1.00</mmcif_mdb:occupancy> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:atom_site> <mmcif_mdb:atom_site id="101"> <mmcif_mdb:B_iso_or_equiv>17.27</mmcif_mdb:B_iso_or_equiv> <mmcif_mdb:Cartn_x>4.171</mmcif_mdb:Cartn_x> <mmcif_mdb:Cartn_y>29.012</mmcif_mdb:Cartn_y> <mmcif_mdb:Cartn_z>7.116</mmcif_mdb:Cartn_z> <mmcif_mdb:auth_seq_id>300</mmcif_mdb:auth_seq_id> <mmcif_mdb:footnote_id>1</mmcif_mdb:footnote_id> <mmcif_mdb:group_PDB>HETATM</mmcif_mdb:group_PDB> <mmcif_mdb:label_alt_id>1</mmcif_mdb:label_alt_id> <mmcif_mdb:label_asym_id>C</mmcif_mdb:label_asym_id> <mmcif_mdb:label_atom_id>C1</mmcif_mdb:label_atom_id> <mmcif_mdb:label_comp_id>APS</mmcif_mdb:label_comp_id> <mmcif_mdb:label_seq_id></mmcif_mdb:label_seq_id> <mmcif_mdb:occupancy>0.58</mmcif_mdb:occupancy> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:atom_site> <mmcif_mdb:atom_site id="102"> <mmcif_mdb:B_iso_or_equiv>16.95</mmcif_mdb:B_iso_or_equiv> <mmcif_mdb:Cartn_x>4.949</mmcif_mdb:Cartn_x> <mmcif_mdb:Cartn_y>27.758</mmcif_mdb:Cartn_y> <mmcif_mdb:Cartn_z>6.793</mmcif_mdb:Cartn_z> <mmcif_mdb:auth_seq_id>300</mmcif_mdb:auth_seq_id> <mmcif_mdb:footnote_id>1</mmcif_mdb:footnote_id> <mmcif_mdb:group_PDB>HETATM</mmcif_mdb:group_PDB> <mmcif_mdb:label_alt_id>1</mmcif_mdb:label_alt_id> <mmcif_mdb:label_asym_id>C</mmcif_mdb:label_asym_id> <mmcif_mdb:label_atom_id>C2</mmcif_mdb:label_atom_id> <mmcif_mdb:label_comp_id>APS</mmcif_mdb:label_comp_id> <mmcif_mdb:label_seq_id></mmcif_mdb:label_seq_id> <mmcif_mdb:occupancy>0.58</mmcif_mdb:occupancy> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:atom_site> <mmcif_mdb:atom_site id="103"> <mmcif_mdb:B_iso_or_equiv>16.85</mmcif_mdb:B_iso_or_equiv> <mmcif_mdb:Cartn_x>4.800</mmcif_mdb:Cartn_x> <mmcif_mdb:Cartn_y>26.678</mmcif_mdb:Cartn_y> <mmcif_mdb:Cartn_z>7.393</mmcif_mdb:Cartn_z> <mmcif_mdb:auth_seq_id>300</mmcif_mdb:auth_seq_id> <mmcif_mdb:footnote_id>1</mmcif_mdb:footnote_id> <mmcif_mdb:group_PDB>HETATM</mmcif_mdb:group_PDB> <mmcif_mdb:label_alt_id>1</mmcif_mdb:label_alt_id> <mmcif_mdb:label_asym_id>C</mmcif_mdb:label_asym_id> <mmcif_mdb:label_atom_id>O3</mmcif_mdb:label_atom_id> <mmcif_mdb:label_comp_id>APS</mmcif_mdb:label_comp_id> <mmcif_mdb:label_seq_id></mmcif_mdb:label_seq_id> <mmcif_mdb:occupancy>0.58</mmcif_mdb:occupancy> <mmcif_mdb:type_symbol>O</mmcif_mdb:type_symbol> </mmcif_mdb:atom_site> <mmcif_mdb:atom_site id="104"> <mmcif_mdb:B_iso_or_equiv>16.43</mmcif_mdb:B_iso_or_equiv> <mmcif_mdb:Cartn_x>5.930</mmcif_mdb:Cartn_x> <mmcif_mdb:Cartn_y>27.841</mmcif_mdb:Cartn_y> <mmcif_mdb:Cartn_z>5.869</mmcif_mdb:Cartn_z> <mmcif_mdb:auth_seq_id>300</mmcif_mdb:auth_seq_id> <mmcif_mdb:footnote_id>1</mmcif_mdb:footnote_id> <mmcif_mdb:group_PDB>HETATM</mmcif_mdb:group_PDB> <mmcif_mdb:label_alt_id>1</mmcif_mdb:label_alt_id> <mmcif_mdb:label_asym_id>C</mmcif_mdb:label_asym_id> <mmcif_mdb:label_atom_id>N4</mmcif_mdb:label_atom_id> <mmcif_mdb:label_comp_id>APS</mmcif_mdb:label_comp_id> <mmcif_mdb:label_seq_id></mmcif_mdb:label_seq_id> <mmcif_mdb:occupancy>0.58</mmcif_mdb:occupancy> <mmcif_mdb:type_symbol>N</mmcif_mdb:type_symbol> </mmcif_mdb:atom_site> </mmcif_mdb:atom_siteCategory> Equivalent isotropic atomic displacement parameter, B~eq~, in angstroms squared, calculated as the geometric mean of the anisotropic atomic displacement parameters. B~eq~ = (B~i~ B~j~ B~k~)^1/3^ B~n~ = the principal components of the orthogonalized 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 standard uncertainty (estimated standard deviation) of attribute B_equiv_geom_mean in category atom_site. Isotropic atomic displacement parameter, or equivalent isotropic atomic displacement parameter, B~eq~, calculated from the anisotropic displacement parameters. B~eq~ = (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 standard uncertainty (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 standard uncertainty (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 standard uncertainty (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 standard uncertainty (estimated standard deviation) of attribute Cartn_z in category atom_site. Equivalent isotropic atomic displacement parameter, U~eq~, in angstroms squared, calculated as the geometric mean of the anisotropic atomic displacement parameters. U~eq~ = (U~i~ U~j~ U~k~)^1/3^ U~n~ = the principal components of the orthogonalized U^ij^ The standard uncertainty (estimated standard deviation) of attribute U_equiv_geom_mean in category atom_site. Isotropic atomic displacement parameter, or equivalent isotropic atomic displacement parameter, U~eq~, calculated from anisotropic atomic displacement parameters. U~eq~ = (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 standard uncertainty (estimated standard deviation) of attribute U_iso_or_equiv in category atom_site. The Wyckoff symbol (letter) as listed in the space-group tables of International Tables for Crystallography, Vol. A (2002). 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 standard uncertainty (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 standard uncertainty (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 standard uncertainty (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 standard uncertainty (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 standard uncertainty (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 standard uncertainty (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 standard uncertainty (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 standard uncertainty (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 standard uncertainty (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 standard uncertainty (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 standard uncertainty (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 standard uncertainty (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 hydrogen 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 whether the site coordinates have been determined from the intensities or calculated from the geometry of surrounding sites, or have been assigned dummy values. 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 which 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 hydrogen 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 standard uncertainty (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 standard uncertainty (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 standard uncertainty (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 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 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 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 identifier for this atom site. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. This data item is a pointer to attribute id in category entity in the ENTITY category. This data item is a pointer to attribute num in category entity_poly_seq in the ENTITY_POLY_SEQ category. The fraction of the atom type present at this site. The sum of the occupancies of all the atom types at this site may not significantly exceed 1.0 unless it is a dummy site. The standard uncertainty (estimated standard deviation) of attribute occupancy in category atom_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 (2002). 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 provide compatibility between small-molecule and macromolecular CIFs. In a small-molecule CIF, _atom_site_label is the identifier for the atom. In a macromolecular CIF, 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 the atoms. For compatibility with older CIFs, _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 anisotropic displacement parameters. 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 [Acta Cryst. (1985), B41, 255-262]. <mmcif_mdb:atom_site_anisotropCategory> <mmcif_mdb:atom_site_anisotrop id="1"> <mmcif_mdb:U11>8642</mmcif_mdb:U11> <mmcif_mdb:U12>4866</mmcif_mdb:U12> <mmcif_mdb:U13>7299</mmcif_mdb:U13> <mmcif_mdb:U22>-342</mmcif_mdb:U22> <mmcif_mdb:U23>-258</mmcif_mdb:U23> <mmcif_mdb:U33>-1427</mmcif_mdb:U33> <mmcif_mdb:type_symbol>O</mmcif_mdb:type_symbol> </mmcif_mdb:atom_site_anisotrop> <mmcif_mdb:atom_site_anisotrop id="2"> <mmcif_mdb:U11>5174</mmcif_mdb:U11> <mmcif_mdb:U12>4871</mmcif_mdb:U12> <mmcif_mdb:U13>6243</mmcif_mdb:U13> <mmcif_mdb:U22>-1885</mmcif_mdb:U22> <mmcif_mdb:U23>-2051</mmcif_mdb:U23> <mmcif_mdb:U33>-1377</mmcif_mdb:U33> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:atom_site_anisotrop> <mmcif_mdb:atom_site_anisotrop id="3"> <mmcif_mdb:U11>6202</mmcif_mdb:U11> <mmcif_mdb:U12>5020</mmcif_mdb:U12> <mmcif_mdb:U13>4395</mmcif_mdb:U13> <mmcif_mdb:U22>-1130</mmcif_mdb:U22> <mmcif_mdb:U23>-556</mmcif_mdb:U23> <mmcif_mdb:U33>-632</mmcif_mdb:U33> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:atom_site_anisotrop> <mmcif_mdb:atom_site_anisotrop id="4"> <mmcif_mdb:U11>4224</mmcif_mdb:U11> <mmcif_mdb:U12>4700</mmcif_mdb:U12> <mmcif_mdb:U13>5046</mmcif_mdb:U13> <mmcif_mdb:U22>1105</mmcif_mdb:U22> <mmcif_mdb:U23>-161</mmcif_mdb:U23> <mmcif_mdb:U33>345</mmcif_mdb:U33> <mmcif_mdb:type_symbol>O</mmcif_mdb:type_symbol> </mmcif_mdb:atom_site_anisotrop> <mmcif_mdb:atom_site_anisotrop id="5"> <mmcif_mdb:U11>8684</mmcif_mdb:U11> <mmcif_mdb:U12>4688</mmcif_mdb:U12> <mmcif_mdb:U13>4171</mmcif_mdb:U13> <mmcif_mdb:U22>-1850</mmcif_mdb:U22> <mmcif_mdb:U23>-433</mmcif_mdb:U23> <mmcif_mdb:U33>-292</mmcif_mdb:U33> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:atom_site_anisotrop> <mmcif_mdb:atom_site_anisotrop id="6"> <mmcif_mdb:U11>11226</mmcif_mdb:U11> <mmcif_mdb:U12>5255</mmcif_mdb:U12> <mmcif_mdb:U13>3532</mmcif_mdb:U13> <mmcif_mdb:U22>-341</mmcif_mdb:U22> <mmcif_mdb:U23>2685</mmcif_mdb:U23> <mmcif_mdb:U33>1328</mmcif_mdb:U33> <mmcif_mdb:type_symbol>O</mmcif_mdb:type_symbol> </mmcif_mdb:atom_site_anisotrop> <mmcif_mdb:atom_site_anisotrop id="7"> <mmcif_mdb:U11>10214</mmcif_mdb:U11> <mmcif_mdb:U12>2428</mmcif_mdb:U12> <mmcif_mdb:U13>5614</mmcif_mdb:U13> <mmcif_mdb:U22>-2610</mmcif_mdb:U22> <mmcif_mdb:U23>-1940</mmcif_mdb:U23> <mmcif_mdb:U33>902</mmcif_mdb:U33> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:atom_site_anisotrop> <mmcif_mdb:atom_site_anisotrop id="8"> <mmcif_mdb:U11>4590</mmcif_mdb:U11> <mmcif_mdb:U12>3488</mmcif_mdb:U12> <mmcif_mdb:U13>5827</mmcif_mdb:U13> <mmcif_mdb:U22>751</mmcif_mdb:U22> <mmcif_mdb:U23>-770</mmcif_mdb:U23> <mmcif_mdb:U33>986</mmcif_mdb:U33> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:atom_site_anisotrop> <mmcif_mdb:atom_site_anisotrop id="9"> <mmcif_mdb:U11>5014</mmcif_mdb:U11> <mmcif_mdb:U12>4434</mmcif_mdb:U12> <mmcif_mdb:U13>3447</mmcif_mdb:U13> <mmcif_mdb:U22>-17</mmcif_mdb:U22> <mmcif_mdb:U23>-1593</mmcif_mdb:U23> <mmcif_mdb:U33>539</mmcif_mdb:U33> <mmcif_mdb:type_symbol>N</mmcif_mdb:type_symbol> </mmcif_mdb:atom_site_anisotrop> </mmcif_mdb: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 standard uncertainty (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 standard uncertainty (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 standard uncertainty (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 standard uncertainty (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 standard uncertainty (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 standard uncertainty (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 standard uncertainty (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 standard uncertainty (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 standard uncertainty (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 standard uncertainty (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 standard uncertainty (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 standard uncertainty (estimated standard deviation) of attribute U[3][3] in category atom_site_anisotrop. 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 laboratory records for the structure corresponding to PDB entry 5HVP. <mmcif_mdb:atom_sitesCategory> <mmcif_mdb:atom_sites entry_id="5HVP"> <mmcif_mdb:Cartn_transf_matrix11>58.39</mmcif_mdb:Cartn_transf_matrix11> <mmcif_mdb:Cartn_transf_matrix12>0.00</mmcif_mdb:Cartn_transf_matrix12> <mmcif_mdb:Cartn_transf_matrix13>0.00</mmcif_mdb:Cartn_transf_matrix13> <mmcif_mdb:Cartn_transf_matrix21>0.00</mmcif_mdb:Cartn_transf_matrix21> <mmcif_mdb:Cartn_transf_matrix22>86.70</mmcif_mdb:Cartn_transf_matrix22> <mmcif_mdb:Cartn_transf_matrix23>0.00</mmcif_mdb:Cartn_transf_matrix23> <mmcif_mdb:Cartn_transf_matrix31>0.00</mmcif_mdb:Cartn_transf_matrix31> <mmcif_mdb:Cartn_transf_matrix32>0.00</mmcif_mdb:Cartn_transf_matrix32> <mmcif_mdb:Cartn_transf_matrix33>46.27</mmcif_mdb:Cartn_transf_matrix33> <mmcif_mdb:Cartn_transf_vector1>0.00</mmcif_mdb:Cartn_transf_vector1> <mmcif_mdb:Cartn_transf_vector2>0.00</mmcif_mdb:Cartn_transf_vector2> <mmcif_mdb:Cartn_transf_vector3>0.00</mmcif_mdb:Cartn_transf_vector3> <mmcif_mdb:Cartn_transform_axes>c along z, astar along x, b along y</mmcif_mdb:Cartn_transform_axes> </mmcif_mdb:atom_sites> </mmcif_mdb: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 three-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 three-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 three-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 and 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][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 [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 three-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 three-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 three-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| This code identifies the method used to locate the hydrogen atoms. *** This data item would not in general be used in a macromolecular data block. *** This code identifies the method used to locate the initial atom sites. *** This data item would not in general be used in a macromolecular data block. *** This code identifies the method used to locate the non-hydrogen-atom sites not found by attribute solution_primary. in category atom_sites *** 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 modelled 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. <mmcif_mdb:atom_sites_altCategory> <mmcif_mdb:atom_sites_alt id="1"> <mmcif_mdb: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.</mmcif_mdb:details> </mmcif_mdb:atom_sites_alt> <mmcif_mdb:atom_sites_alt id="2"> <mmcif_mdb: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.</mmcif_mdb:details> </mmcif_mdb:atom_sites_alt> <mmcif_mdb:atom_sites_alt id="3"> <mmcif_mdb: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.</mmcif_mdb:details> </mmcif_mdb:atom_sites_alt> <mmcif_mdb:atom_sites_alt id="4"> <mmcif_mdb: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.</mmcif_mdb:details> </mmcif_mdb:atom_sites_alt> </mmcif_mdb:atom_sites_altCategory> A description of special aspects of the modelling 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. <mmcif_mdb:atom_sites_alt_ensCategory> <mmcif_mdb:atom_sites_alt_ens id="Ensemble 1-A"> <mmcif_mdb: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.</mmcif_mdb:details> </mmcif_mdb:atom_sites_alt_ens> <mmcif_mdb:atom_sites_alt_ens id="Ensemble 1-B"> <mmcif_mdb: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.</mmcif_mdb:details> </mmcif_mdb:atom_sites_alt_ens> <mmcif_mdb:atom_sites_alt_ens id="Ensemble 2-A"> <mmcif_mdb: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.</mmcif_mdb:details> </mmcif_mdb:atom_sites_alt_ens> <mmcif_mdb:atom_sites_alt_ens id="Ensemble 2-B"> <mmcif_mdb: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.</mmcif_mdb:details> </mmcif_mdb:atom_sites_alt_ens> </mmcif_mdb: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. <mmcif_mdb:atom_sites_alt_genCategory> <mmcif_mdb:atom_sites_alt_gen alt_id="1" ens_id="Ensemble 1-A"></mmcif_mdb:atom_sites_alt_gen> <mmcif_mdb:atom_sites_alt_gen alt_id="3" ens_id="Ensemble 1-A"></mmcif_mdb:atom_sites_alt_gen> <mmcif_mdb:atom_sites_alt_gen alt_id="1" ens_id="Ensemble 1-B"></mmcif_mdb:atom_sites_alt_gen> <mmcif_mdb:atom_sites_alt_gen alt_id="4" ens_id="Ensemble 1-B"></mmcif_mdb:atom_sites_alt_gen> <mmcif_mdb:atom_sites_alt_gen alt_id="2" ens_id="Ensemble 2-A"></mmcif_mdb:atom_sites_alt_gen> <mmcif_mdb:atom_sites_alt_gen alt_id="3" ens_id="Ensemble 2-A"></mmcif_mdb:atom_sites_alt_gen> <mmcif_mdb:atom_sites_alt_gen alt_id="2" ens_id="Ensemble 2-B"></mmcif_mdb:atom_sites_alt_gen> <mmcif_mdb:atom_sites_alt_gen alt_id="4" ens_id="Ensemble 2-B"></mmcif_mdb:atom_sites_alt_gen> </mmcif_mdb:atom_sites_alt_genCategory> This data item is a pointer to attribute id in category atom_sites_alt in the ATOM_SITES_ALT category. This data item is a pointer to attribute id in category atom_sites_alt_ens in the ATOM_SITES_ALT_ENS category. Data items in the ATOM_SITES_FOOTNOTE category record detailed comments about an atom site or a group of atom sites. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <mmcif_mdb:atom_sites_footnoteCategory> <mmcif_mdb:atom_sites_footnote id="1"> <mmcif_mdb:text> The inhibitor binds to the enzyme in two alternative orientations. The two orientations have been assigned alternative IDs *1* and *2*.</mmcif_mdb:text> </mmcif_mdb:atom_sites_footnote> <mmcif_mdb:atom_sites_footnote id="2"> <mmcif_mdb: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*.</mmcif_mdb:text> </mmcif_mdb:atom_sites_footnote> <mmcif_mdb:atom_sites_footnote id="3"> <mmcif_mdb: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*.</mmcif_mdb:text> </mmcif_mdb:atom_sites_footnote> <mmcif_mdb:atom_sites_footnote id="4"> <mmcif_mdb:text> Side chains of these residues adopt alternative orientations that do not correlate with the alternative orientation of the inhibitor.</mmcif_mdb:text> </mmcif_mdb:atom_sites_footnote> <mmcif_mdb:atom_sites_footnote id="5"> <mmcif_mdb: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.</mmcif_mdb:text> </mmcif_mdb:atom_sites_footnote> </mmcif_mdb:atom_sites_footnoteCategory> The text of the footnote. Footnotes are used to describe an atom site or a 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 modelled. A code that identifies the footnote. a b 1 2 Data items in the ATOM_TYPE category record details about the 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. <mmcif_mdb:atom_typeCategory> <mmcif_mdb:atom_type symbol="C"> <mmcif_mdb:oxidation_number>0</mmcif_mdb:oxidation_number> <mmcif_mdb:scat_Cromer_Mann_a1>2.31000</mmcif_mdb:scat_Cromer_Mann_a1> <mmcif_mdb:scat_Cromer_Mann_a2>20.8439</mmcif_mdb:scat_Cromer_Mann_a2> <mmcif_mdb:scat_Cromer_Mann_a3>1.02000</mmcif_mdb:scat_Cromer_Mann_a3> <mmcif_mdb:scat_Cromer_Mann_a4>10.2075</mmcif_mdb:scat_Cromer_Mann_a4> <mmcif_mdb:scat_Cromer_Mann_b1>1.58860</mmcif_mdb:scat_Cromer_Mann_b1> <mmcif_mdb:scat_Cromer_Mann_b2>0.568700</mmcif_mdb:scat_Cromer_Mann_b2> <mmcif_mdb:scat_Cromer_Mann_b3>0.865000</mmcif_mdb:scat_Cromer_Mann_b3> <mmcif_mdb:scat_Cromer_Mann_b4>51.6512</mmcif_mdb:scat_Cromer_Mann_b4> <mmcif_mdb:scat_Cromer_Mann_c>0.21560</mmcif_mdb:scat_Cromer_Mann_c> </mmcif_mdb:atom_type> <mmcif_mdb:atom_type symbol="N"> <mmcif_mdb:oxidation_number>0</mmcif_mdb:oxidation_number> <mmcif_mdb:scat_Cromer_Mann_a1>12.2126</mmcif_mdb:scat_Cromer_Mann_a1> <mmcif_mdb:scat_Cromer_Mann_a2>0.005700</mmcif_mdb:scat_Cromer_Mann_a2> <mmcif_mdb:scat_Cromer_Mann_a3>3.13220</mmcif_mdb:scat_Cromer_Mann_a3> <mmcif_mdb:scat_Cromer_Mann_a4>9.89330</mmcif_mdb:scat_Cromer_Mann_a4> <mmcif_mdb:scat_Cromer_Mann_b1>2.01250</mmcif_mdb:scat_Cromer_Mann_b1> <mmcif_mdb:scat_Cromer_Mann_b2>28.9975</mmcif_mdb:scat_Cromer_Mann_b2> <mmcif_mdb:scat_Cromer_Mann_b3>1.16630</mmcif_mdb:scat_Cromer_Mann_b3> <mmcif_mdb:scat_Cromer_Mann_b4>0.582600</mmcif_mdb:scat_Cromer_Mann_b4> <mmcif_mdb:scat_Cromer_Mann_c>-11.529</mmcif_mdb:scat_Cromer_Mann_c> </mmcif_mdb:atom_type> <mmcif_mdb:atom_type symbol="O"> <mmcif_mdb:oxidation_number>0</mmcif_mdb:oxidation_number> <mmcif_mdb:scat_Cromer_Mann_a1>3.04850</mmcif_mdb:scat_Cromer_Mann_a1> <mmcif_mdb:scat_Cromer_Mann_a2>13.2771</mmcif_mdb:scat_Cromer_Mann_a2> <mmcif_mdb:scat_Cromer_Mann_a3>2.28680</mmcif_mdb:scat_Cromer_Mann_a3> <mmcif_mdb:scat_Cromer_Mann_a4>5.70110</mmcif_mdb:scat_Cromer_Mann_a4> <mmcif_mdb:scat_Cromer_Mann_b1>1.54630</mmcif_mdb:scat_Cromer_Mann_b1> <mmcif_mdb:scat_Cromer_Mann_b2>0.323900</mmcif_mdb:scat_Cromer_Mann_b2> <mmcif_mdb:scat_Cromer_Mann_b3>0.867000</mmcif_mdb:scat_Cromer_Mann_b3> <mmcif_mdb:scat_Cromer_Mann_b4>32.9089</mmcif_mdb:scat_Cromer_Mann_b4> <mmcif_mdb:scat_Cromer_Mann_c>0.250800</mmcif_mdb:scat_Cromer_Mann_c> </mmcif_mdb:atom_type> <mmcif_mdb:atom_type symbol="S"> <mmcif_mdb:oxidation_number>0</mmcif_mdb:oxidation_number> <mmcif_mdb:scat_Cromer_Mann_a1>6.90530</mmcif_mdb:scat_Cromer_Mann_a1> <mmcif_mdb:scat_Cromer_Mann_a2>1.46790</mmcif_mdb:scat_Cromer_Mann_a2> <mmcif_mdb:scat_Cromer_Mann_a3>5.20340</mmcif_mdb:scat_Cromer_Mann_a3> <mmcif_mdb:scat_Cromer_Mann_a4>22.2151</mmcif_mdb:scat_Cromer_Mann_a4> <mmcif_mdb:scat_Cromer_Mann_b1>1.43790</mmcif_mdb:scat_Cromer_Mann_b1> <mmcif_mdb:scat_Cromer_Mann_b2>0.253600</mmcif_mdb:scat_Cromer_Mann_b2> <mmcif_mdb:scat_Cromer_Mann_b3>1.58630</mmcif_mdb:scat_Cromer_Mann_b3> <mmcif_mdb:scat_Cromer_Mann_b4>56.1720</mmcif_mdb:scat_Cromer_Mann_b4> <mmcif_mdb:scat_Cromer_Mann_c>0.866900</mmcif_mdb:scat_Cromer_Mann_c> </mmcif_mdb:atom_type> <mmcif_mdb:atom_type symbol="CL"> <mmcif_mdb:oxidation_number>-1</mmcif_mdb:oxidation_number> <mmcif_mdb:scat_Cromer_Mann_a1>18.2915</mmcif_mdb:scat_Cromer_Mann_a1> <mmcif_mdb:scat_Cromer_Mann_a2>0.006600</mmcif_mdb:scat_Cromer_Mann_a2> <mmcif_mdb:scat_Cromer_Mann_a3>7.20840</mmcif_mdb:scat_Cromer_Mann_a3> <mmcif_mdb:scat_Cromer_Mann_a4>1.17170</mmcif_mdb:scat_Cromer_Mann_a4> <mmcif_mdb:scat_Cromer_Mann_b1>6.53370</mmcif_mdb:scat_Cromer_Mann_b1> <mmcif_mdb:scat_Cromer_Mann_b2>19.5424</mmcif_mdb:scat_Cromer_Mann_b2> <mmcif_mdb:scat_Cromer_Mann_b3>2.33860</mmcif_mdb:scat_Cromer_Mann_b3> <mmcif_mdb:scat_Cromer_Mann_b4>60.4486</mmcif_mdb:scat_Cromer_Mann_b4> <mmcif_mdb:scat_Cromer_Mann_c>-16.378</mmcif_mdb:scat_Cromer_Mann_c> </mmcif_mdb:atom_type> </mmcif_mdb:atom_typeCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <mmcif_mdb:atom_typeCategory> <mmcif_mdb:atom_type symbol="C"> <mmcif_mdb:number_in_cell>72</mmcif_mdb:number_in_cell> <mmcif_mdb:oxidation_number>0</mmcif_mdb:oxidation_number> <mmcif_mdb:scat_dispersion_imag>.009</mmcif_mdb:scat_dispersion_imag> <mmcif_mdb:scat_dispersion_real>.017</mmcif_mdb:scat_dispersion_real> <mmcif_mdb:scat_source>International_Tables_Vol_IV_Table_2.2B</mmcif_mdb:scat_source> </mmcif_mdb:atom_type> <mmcif_mdb:atom_type symbol="H"> <mmcif_mdb:number_in_cell>100</mmcif_mdb:number_in_cell> <mmcif_mdb:oxidation_number>0</mmcif_mdb:oxidation_number> <mmcif_mdb:scat_dispersion_imag>0</mmcif_mdb:scat_dispersion_imag> <mmcif_mdb:scat_dispersion_real>0</mmcif_mdb:scat_dispersion_real> <mmcif_mdb:scat_source>International_Tables_Vol_IV_Table_2.2B</mmcif_mdb:scat_source> </mmcif_mdb:atom_type> <mmcif_mdb:atom_type symbol="O"> <mmcif_mdb:number_in_cell>12</mmcif_mdb:number_in_cell> <mmcif_mdb:oxidation_number>0</mmcif_mdb:oxidation_number> <mmcif_mdb:scat_dispersion_imag>.032</mmcif_mdb:scat_dispersion_imag> <mmcif_mdb:scat_dispersion_real>.047</mmcif_mdb:scat_dispersion_real> <mmcif_mdb:scat_source>International_Tables_Vol_IV_Table_2.2B</mmcif_mdb:scat_source> </mmcif_mdb:atom_type> <mmcif_mdb:atom_type symbol="N"> <mmcif_mdb:number_in_cell>4</mmcif_mdb:number_in_cell> <mmcif_mdb:oxidation_number>0</mmcif_mdb:oxidation_number> <mmcif_mdb:scat_dispersion_imag>.018</mmcif_mdb:scat_dispersion_imag> <mmcif_mdb:scat_dispersion_real>.029</mmcif_mdb:scat_dispersion_real> <mmcif_mdb:scat_source>International_Tables_Vol_IV_Table_2.2B</mmcif_mdb:scat_source> </mmcif_mdb:atom_type> </mmcif_mdb: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 Cromer-Mann scattering-factor coefficient a1 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. The Cromer-Mann scattering-factor coefficient a2 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. The Cromer-Mann scattering-factor coefficient a3 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. The Cromer-Mann scattering-factor coefficient a4 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. The Cromer-Mann scattering-factor coefficient b1 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. The Cromer-Mann scattering-factor coefficient b2 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. The Cromer-Mann scattering-factor coefficient b3 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. The Cromer-Mann scattering-factor coefficient b4 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. The Cromer-Mann scattering-factor coefficient c used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. The imaginary component of the anomalous-dispersion scattering factor, 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 factor, 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 the source of the scattering factors or scattering lengths 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 species (singular or plural) representing this atom type. Normally this code is the element symbol. The code may be composed of any character except an underscore 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 record different stages in the 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. <mmcif_mdb:auditCategory> <mmcif_mdb:audit revision_id="1"> <mmcif_mdb:creation_date>1992-12-08</mmcif_mdb:creation_date> <mmcif_mdb:creation_method> Created by hand from PDB entry 5HVP, from the J. Biol. Chem. paper describing this structure and from laboratory records</mmcif_mdb:creation_method> <mmcif_mdb:update_record> 1992-12-09 adjusted to reflect comments from B. McKeever 1992-12-10 adjusted to reflect comments from H. Berman 1992-12-12 adjusted to reflect comments from K. Watenpaugh</mmcif_mdb:update_record> </mmcif_mdb:audit> </mmcif_mdb:auditCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. 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. <mmcif_mdb:audit_authorCategory> <mmcif_mdb:audit_author name="Fitzgerald, Paula M.D."> <mmcif_mdb:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</mmcif_mdb:address> </mmcif_mdb:audit_author> <mmcif_mdb:audit_author name="McKeever, Brian M."> <mmcif_mdb:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</mmcif_mdb:address> </mmcif_mdb:audit_author> <mmcif_mdb:audit_author name="Van Middlesworth, J.F."> <mmcif_mdb:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</mmcif_mdb:address> </mmcif_mdb:audit_author> <mmcif_mdb:audit_author name="Springer, James P."> <mmcif_mdb:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</mmcif_mdb:address> </mmcif_mdb:audit_author> </mmcif_mdb: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 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 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. <mmcif_mdb:audit_conformCategory> <mmcif_mdb:audit_conform dict_name="cif_core.dic" dict_version="2.3.1"> <mmcif_mdb:dict_location>ftp://ftp.iucr.org/pub/cif_core.2.3.1.dic</mmcif_mdb:dict_location> </mmcif_mdb:audit_conform> </mmcif_mdb:audit_conformCategory> A file name or uniform resource locator (URL) for the dictionary to which the current data block conforms. The string identifying the highest-level dictionary defining data names used in this file. The version number of the dictionary to which the current data block conforms. Data items in the AUDIT_CONTACT_AUTHOR category record details about the name and address of the author to be contacted concerning the content of this data block. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <mmcif_mdb:audit_contact_authorCategory> <mmcif_mdb:audit_contact_author name="Fitzgerald, Paula M.D."> <mmcif_mdb:address> Department of Biophysical Chemistry Merck Research Laboratories PO Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</mmcif_mdb:address> <mmcif_mdb:email>paula_fitzgerald@merck.com</mmcif_mdb:email> <mmcif_mdb:fax>1(908)5946645</mmcif_mdb:fax> <mmcif_mdb:phone>1(908)5945510</mmcif_mdb:phone> </mmcif_mdb:audit_contact_author> </mmcif_mdb: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 recognizable to international networks. The format of e-mail addresses is given in Section 3.4, Address Specification, of Internet Message Format, RFC 2822, P. Resnick (Editor), Network Standards Group, April 2001. name@host.domain.country bm@iucr.org The facsimile telephone number of the author of the data block to whom correspondence should be addressed. The recommended style starts with the international dialing prefix, followed by the area code in parentheses, followed by the local number with no spaces. 12(34)9477334 12()349477334 The telephone number of the author of the data block to whom correspondence should be addressed. The recommended style starts with the international dialing prefix, followed by the area code in parentheses, followed by the local number and any extension number prefixed by 'x', with no spaces. 12(34)9477330 12()349477330 12(34)9477330x5543 The name of the author of the data block to whom correspondence should be addressed. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s). Bleary, Percival R. O'Neil, F.K. Van den Bossche, G. Yang, D.-L. Simonov, Yu.A Data items in the CELL category record details about the crystallographic cell parameters. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <mmcif_mdb:cellCategory> <mmcif_mdb:cell entry_id="5HVP"> <mmcif_mdb:angle_alpha>90.00</mmcif_mdb:angle_alpha> <mmcif_mdb:angle_beta>90.00</mmcif_mdb:angle_beta> <mmcif_mdb:angle_gamma>90.00</mmcif_mdb:angle_gamma> <mmcif_mdb: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.</mmcif_mdb:details> <mmcif_mdb:length_a>58.39</mmcif_mdb:length_a> <mmcif_mdb:length_a_esd>0.05</mmcif_mdb:length_a_esd> <mmcif_mdb:length_b>86.70</mmcif_mdb:length_b> <mmcif_mdb:length_b_esd>0.12</mmcif_mdb:length_b_esd> <mmcif_mdb:length_c>46.27</mmcif_mdb:length_c> <mmcif_mdb:length_c_esd>0.06</mmcif_mdb:length_c_esd> <mmcif_mdb:volume>234237</mmcif_mdb:volume> </mmcif_mdb:cell> </mmcif_mdb:cellCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. 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 of the reported structure in degrees. The standard uncertainty (estimated standard deviation) of attribute angle_alpha in category cell. Unit-cell angle beta of the reported structure in degrees. The standard uncertainty (estimated standard deviation) of attribute angle_beta in category cell. Unit-cell angle gamma of the reported structure in degrees. The standard uncertainty (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 in angstroms. The standard uncertainty (estimated standard deviation) of attribute length_a in category cell. Unit-cell length b corresponding to the structure reported in angstroms. The standard uncertainty (estimated standard deviation) of attribute length_b in category cell. Unit-cell length c corresponding to the structure reported in angstroms. The standard uncertainty (estimated standard deviation) of attribute length_c in category cell. 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 standard uncertainty (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. <mmcif_mdb:cell_measurementCategory> <mmcif_mdb:cell_measurement entry_id="5HVP"> <mmcif_mdb:temp>293</mmcif_mdb:temp> <mmcif_mdb:temp_esd>3</mmcif_mdb:temp_esd> <mmcif_mdb:theta_max>31</mmcif_mdb:theta_max> <mmcif_mdb:theta_min>11</mmcif_mdb:theta_min> <mmcif_mdb:wavelength>1.54</mmcif_mdb:wavelength> </mmcif_mdb:cell_measurement> </mmcif_mdb:cell_measurementCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. The pressure in kilopascals at which the unit-cell parameters were measured (not the pressure at which the sample was synthesized). The standard uncertainty (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 standard uncertainty (estimated standard deviation) of attribute temp in category cell_measurement. The maximum theta angle of reflections used to measure the unit cell in degrees. The minimum theta angle of reflections used to measure the unit cell in degrees. 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 to determine 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 (unpublished). <mmcif_mdb:cell_measurement_reflnCategory> <mmcif_mdb:cell_measurement_refln index_h="-2" index_k="4" index_l="1"> <mmcif_mdb:theta>8.67</mmcif_mdb:theta> </mmcif_mdb:cell_measurement_refln> <mmcif_mdb:cell_measurement_refln index_h="0" index_k="3" index_l="2"> <mmcif_mdb:theta>9.45</mmcif_mdb:theta> </mmcif_mdb:cell_measurement_refln> <mmcif_mdb:cell_measurement_refln index_h="3" index_k="0" index_l="2"> <mmcif_mdb:theta>9.46</mmcif_mdb:theta> </mmcif_mdb:cell_measurement_refln> <mmcif_mdb:cell_measurement_refln index_h="-3" index_k="4" index_l="1"> <mmcif_mdb:theta>8.93</mmcif_mdb:theta> </mmcif_mdb:cell_measurement_refln> <mmcif_mdb:cell_measurement_refln index_h="-2" index_k="1" index_l="-2"> <mmcif_mdb:theta>7.53</mmcif_mdb:theta> </mmcif_mdb:cell_measurement_refln> <mmcif_mdb:cell_measurement_refln index_h="10" index_k="0" index_l="0"> <mmcif_mdb:theta>23.77</mmcif_mdb:theta> </mmcif_mdb:cell_measurement_refln> <mmcif_mdb:cell_measurement_refln index_h="0" index_k="10" index_l="0"> <mmcif_mdb:theta>23.78</mmcif_mdb:theta> </mmcif_mdb:cell_measurement_refln> <mmcif_mdb:cell_measurement_refln index_h="-5" index_k="4" index_l="1"> <mmcif_mdb:theta>11.14</mmcif_mdb:theta> </mmcif_mdb:cell_measurement_refln> </mmcif_mdb:cell_measurement_reflnCategory> Theta angle for a reflection used for measurement of the unit cell in degrees. 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 about each of the chemical components from which the relevant chemical structures can be constructed, such as name, mass or charge. 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. <mmcif_mdb:chem_compCategory> <mmcif_mdb:chem_comp id="phe"> <mmcif_mdb:model_source>1987 Protin/Prolsq Ideals file</mmcif_mdb:model_source> <mmcif_mdb:name>phenylalanine</mmcif_mdb:name> </mmcif_mdb:chem_comp> <mmcif_mdb:chem_comp id="val"> <mmcif_mdb:model_source>1987 Protin/Prolsq Ideals file</mmcif_mdb:model_source> <mmcif_mdb:name>alanine</mmcif_mdb:name> </mmcif_mdb:chem_comp> </mmcif_mdb:chem_compCategory> The formula for the chemical component. Formulae are written according to the following rules: (1) Only recognized 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), but in general parentheses are not used. (4) The order of elements depends on whether carbon is present or not. 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 from which the atomic description of the component is taken. 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 nonstandard monomer if the nonstandard monomer 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 nonstandard monomer. 'yes' indicates that this is a 'standard' monomer, 'no' indicates that it is 'nonstandard'. Nonstandard monomers should be described in more detail using the _chem_comp.mon_nstd_parent, _chem_comp.mon_nstd_class and attribute mon_nstd_details in category chem_comp data items. The name of the parent monomer of the nonstandard monomer, if the nonstandard monomer represents a modification of a standard monomer. tyrosine cytosine The identifier for the parent component of the nonstandard component. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. The full name of the component. alanine valine adenine cytosine The total number of atoms in the component. The number of non-hydrogen atoms in the component. For standard polymer components, the one-letter code for the component. If there is not a standard one-letter code for this component, or if this is a non-polymer component, the one-letter code should be given as 'X'. This code may be preceded by a '+' character to indicate that the component is a modification of a standard component. alanine or adenine A ambiguous asparagine/aspartic acid B arginine R asparagine N aspartic acid D cysteine or cystine or cytosine C glutamine Q glutamic acid E ambiguous glutamine/glutamic acid Z glycine or guanine G histidine H isoleucine I leucine L lysine K methionine M phenylalanine F proline P serine S threonine or thymine T tryptophan W tyrosine Y valine V uracil U water O other X 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-methylcytosine 5MC 2(prime)-O-methylcytodine OMC 1-methylguanosine 1MG N(2)-methylguanosine 2MG N(2)-dimethylguanosine M2G 7-methylguanosine 7MG 2(prime)-O-methylguanosine 0MG dihydrouridine 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 the amino acid. For nucleic acid polymer entities, this is the one-letter code for the base. 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. <mmcif_mdb:chem_comp_angleCategory> <mmcif_mdb:chem_comp_angle atom_id_1="N" atom_id_2="CA" atom_id_3="C" comp_id="phe"> <mmcif_mdb:value_angle>xxx.xx</mmcif_mdb:value_angle> <mmcif_mdb:value_dist>x.xx</mmcif_mdb:value_dist> </mmcif_mdb:chem_comp_angle> <mmcif_mdb:chem_comp_angle atom_id_1="CA" atom_id_2="C" atom_id_3="O" comp_id="phe"> <mmcif_mdb:value_angle>xxx.xx</mmcif_mdb:value_angle> <mmcif_mdb:value_dist>x.xx</mmcif_mdb:value_dist> </mmcif_mdb:chem_comp_angle> <mmcif_mdb:chem_comp_angle atom_id_1="CB" atom_id_2="CA" atom_id_3="C" comp_id="phe"> <mmcif_mdb:value_angle>xxx.xx</mmcif_mdb:value_angle> <mmcif_mdb:value_dist>x.xx</mmcif_mdb:value_dist> </mmcif_mdb:chem_comp_angle> <mmcif_mdb:chem_comp_angle atom_id_1="CB" atom_id_2="CA" atom_id_3="N" comp_id="phe"> <mmcif_mdb:value_angle>xxx.xx</mmcif_mdb:value_angle> <mmcif_mdb:value_dist>x.xx</mmcif_mdb:value_dist> </mmcif_mdb:chem_comp_angle> <mmcif_mdb:chem_comp_angle atom_id_1="CA" atom_id_2="CB" atom_id_3="CG" comp_id="phe"> <mmcif_mdb:value_angle>xxx.xx</mmcif_mdb:value_angle> <mmcif_mdb:value_dist>x.xx</mmcif_mdb:value_dist> </mmcif_mdb:chem_comp_angle> <mmcif_mdb:chem_comp_angle atom_id_1="CB" atom_id_2="CG" atom_id_3="CD1" comp_id="phe"> <mmcif_mdb:value_angle>xxx.xx</mmcif_mdb:value_angle> <mmcif_mdb:value_dist>x.xx</mmcif_mdb:value_dist> </mmcif_mdb:chem_comp_angle> <mmcif_mdb:chem_comp_angle atom_id_1="CB" atom_id_2="CG" atom_id_3="CD2" comp_id="phe"> <mmcif_mdb:value_angle>xxx.xx</mmcif_mdb:value_angle> <mmcif_mdb:value_dist>x.xx</mmcif_mdb:value_dist> </mmcif_mdb:chem_comp_angle> <mmcif_mdb:chem_comp_angle atom_id_1="CD1" atom_id_2="CG" atom_id_3="CD2" comp_id="phe"> <mmcif_mdb:value_angle>xxx.xx</mmcif_mdb:value_angle> <mmcif_mdb:value_dist>x.xx</mmcif_mdb:value_dist> </mmcif_mdb:chem_comp_angle> <mmcif_mdb:chem_comp_angle atom_id_1="CG" atom_id_2="CD1" atom_id_3="CE1" comp_id="phe"> <mmcif_mdb:value_angle>xxx.xx</mmcif_mdb:value_angle> <mmcif_mdb:value_dist>x.xx</mmcif_mdb:value_dist> </mmcif_mdb:chem_comp_angle> <mmcif_mdb:chem_comp_angle atom_id_1="CD1" atom_id_2="CE1" atom_id_3="CZ" comp_id="phe"> <mmcif_mdb:value_angle>xxx.xx</mmcif_mdb:value_angle> <mmcif_mdb:value_dist>x.xx</mmcif_mdb:value_dist> </mmcif_mdb:chem_comp_angle> <mmcif_mdb:chem_comp_angle atom_id_1="CE1" atom_id_2="CZ" atom_id_3="CE2" comp_id="phe"> <mmcif_mdb:value_angle>xxx.xx</mmcif_mdb:value_angle> <mmcif_mdb:value_dist>x.xx</mmcif_mdb:value_dist> </mmcif_mdb:chem_comp_angle> <mmcif_mdb:chem_comp_angle atom_id_1="CZ" atom_id_2="CE2" atom_id_3="CD2" comp_id="phe"> <mmcif_mdb:value_angle>xxx.xx</mmcif_mdb:value_angle> <mmcif_mdb:value_dist>x.xx</mmcif_mdb:value_dist> </mmcif_mdb:chem_comp_angle> <mmcif_mdb:chem_comp_angle atom_id_1="CG" atom_id_2="CD2" atom_id_3="CE2" comp_id="phe"> <mmcif_mdb:value_angle>xxx.xx</mmcif_mdb:value_angle> <mmcif_mdb:value_dist>x.xx</mmcif_mdb:value_dist> </mmcif_mdb:chem_comp_angle> <mmcif_mdb:chem_comp_angle atom_id_1="N" atom_id_2="CA" atom_id_3="C" comp_id="val"> <mmcif_mdb:value_angle>xxx.xx</mmcif_mdb:value_angle> <mmcif_mdb:value_dist>x.xx</mmcif_mdb:value_dist> </mmcif_mdb:chem_comp_angle> <mmcif_mdb:chem_comp_angle atom_id_1="CA" atom_id_2="C" atom_id_3="O" comp_id="val"> <mmcif_mdb:value_angle>xxx.xx</mmcif_mdb:value_angle> <mmcif_mdb:value_dist>x.xx</mmcif_mdb:value_dist> </mmcif_mdb:chem_comp_angle> <mmcif_mdb:chem_comp_angle atom_id_1="CB" atom_id_2="CA" atom_id_3="C" comp_id="val"> <mmcif_mdb:value_angle>xxx.xx</mmcif_mdb:value_angle> <mmcif_mdb:value_dist>x.xx</mmcif_mdb:value_dist> </mmcif_mdb:chem_comp_angle> <mmcif_mdb:chem_comp_angle atom_id_1="CB" atom_id_2="CA" atom_id_3="N" comp_id="val"> <mmcif_mdb:value_angle>xxx.xx</mmcif_mdb:value_angle> <mmcif_mdb:value_dist>x.xx</mmcif_mdb:value_dist> </mmcif_mdb:chem_comp_angle> <mmcif_mdb:chem_comp_angle atom_id_1="CA" atom_id_2="CB" atom_id_3="CG1" comp_id="val"> <mmcif_mdb:value_angle>xxx.xx</mmcif_mdb:value_angle> <mmcif_mdb:value_dist>x.xx</mmcif_mdb:value_dist> </mmcif_mdb:chem_comp_angle> <mmcif_mdb:chem_comp_angle atom_id_1="CA" atom_id_2="CB" atom_id_3="CG2" comp_id="val"> <mmcif_mdb:value_angle>xxx.xx</mmcif_mdb:value_angle> <mmcif_mdb:value_dist>x.xx</mmcif_mdb:value_dist> </mmcif_mdb:chem_comp_angle> <mmcif_mdb:chem_comp_angle atom_id_1="CG1" atom_id_2="CB" atom_id_3="CG2" comp_id="val"> <mmcif_mdb:value_angle>xxx.xx</mmcif_mdb:value_angle> <mmcif_mdb:value_dist>x.xx</mmcif_mdb:value_dist> </mmcif_mdb:chem_comp_angle> </mmcif_mdb: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 standard uncertainty (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 standard uncertainty (estimated standard deviation) of attribute value_dist in category chem_comp_angle. 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. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. Data items in the CHEM_COMP_ATOM category record details about the atoms in a chemical component. Specifying the atomic coordinates for the components in this category 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. <mmcif_mdb:chem_comp_atomCategory> <mmcif_mdb:chem_comp_atom atom_id="N" comp_id="phe"> <mmcif_mdb:model_Cartn_x>1.20134</mmcif_mdb:model_Cartn_x> <mmcif_mdb:model_Cartn_y>0.84658</mmcif_mdb:model_Cartn_y> <mmcif_mdb:model_Cartn_z>0.00000</mmcif_mdb:model_Cartn_z> <mmcif_mdb:substruct_code>main</mmcif_mdb:substruct_code> <mmcif_mdb:type_symbol>N</mmcif_mdb:type_symbol> </mmcif_mdb:chem_comp_atom> <mmcif_mdb:chem_comp_atom atom_id="CA" comp_id="phe"> <mmcif_mdb:model_Cartn_x>0.00000</mmcif_mdb:model_Cartn_x> <mmcif_mdb:model_Cartn_y>0.00000</mmcif_mdb:model_Cartn_y> <mmcif_mdb:model_Cartn_z>0.00000</mmcif_mdb:model_Cartn_z> <mmcif_mdb:substruct_code>main</mmcif_mdb:substruct_code> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:chem_comp_atom> <mmcif_mdb:chem_comp_atom atom_id="C" comp_id="phe"> <mmcif_mdb:model_Cartn_x>-1.25029</mmcif_mdb:model_Cartn_x> <mmcif_mdb:model_Cartn_y>0.88107</mmcif_mdb:model_Cartn_y> <mmcif_mdb:model_Cartn_z>0.00000</mmcif_mdb:model_Cartn_z> <mmcif_mdb:substruct_code>main</mmcif_mdb:substruct_code> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:chem_comp_atom> <mmcif_mdb:chem_comp_atom atom_id="O" comp_id="phe"> <mmcif_mdb:model_Cartn_x>-2.18525</mmcif_mdb:model_Cartn_x> <mmcif_mdb:model_Cartn_y>0.66029</mmcif_mdb:model_Cartn_y> <mmcif_mdb:model_Cartn_z>-0.78409</mmcif_mdb:model_Cartn_z> <mmcif_mdb:substruct_code>main</mmcif_mdb:substruct_code> <mmcif_mdb:type_symbol>O</mmcif_mdb:type_symbol> </mmcif_mdb:chem_comp_atom> <mmcif_mdb:chem_comp_atom atom_id="CB" comp_id="phe"> <mmcif_mdb:model_Cartn_x>0.00662</mmcif_mdb:model_Cartn_x> <mmcif_mdb:model_Cartn_y>-1.03603</mmcif_mdb:model_Cartn_y> <mmcif_mdb:model_Cartn_z>1.11081</mmcif_mdb:model_Cartn_z> <mmcif_mdb:substruct_code>side</mmcif_mdb:substruct_code> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:chem_comp_atom> <mmcif_mdb:chem_comp_atom atom_id="CG" comp_id="phe"> <mmcif_mdb:model_Cartn_x>0.03254</mmcif_mdb:model_Cartn_x> <mmcif_mdb:model_Cartn_y>-0.49711</mmcif_mdb:model_Cartn_y> <mmcif_mdb:model_Cartn_z>2.50951</mmcif_mdb:model_Cartn_z> <mmcif_mdb:substruct_code>side</mmcif_mdb:substruct_code> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:chem_comp_atom> <mmcif_mdb:chem_comp_atom atom_id="CD1" comp_id="phe"> <mmcif_mdb:model_Cartn_x>-1.15813</mmcif_mdb:model_Cartn_x> <mmcif_mdb:model_Cartn_y>-0.12084</mmcif_mdb:model_Cartn_y> <mmcif_mdb:model_Cartn_z>3.13467</mmcif_mdb:model_Cartn_z> <mmcif_mdb:substruct_code>side</mmcif_mdb:substruct_code> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:chem_comp_atom> <mmcif_mdb:chem_comp_atom atom_id="CE1" comp_id="phe"> <mmcif_mdb:model_Cartn_x>-1.15720</mmcif_mdb:model_Cartn_x> <mmcif_mdb:model_Cartn_y>0.38038</mmcif_mdb:model_Cartn_y> <mmcif_mdb:model_Cartn_z>4.42732</mmcif_mdb:model_Cartn_z> <mmcif_mdb:substruct_code>side</mmcif_mdb:substruct_code> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:chem_comp_atom> <mmcif_mdb:chem_comp_atom atom_id="CZ" comp_id="phe"> <mmcif_mdb:model_Cartn_x>0.05385</mmcif_mdb:model_Cartn_x> <mmcif_mdb:model_Cartn_y>0.51332</mmcif_mdb:model_Cartn_y> <mmcif_mdb:model_Cartn_z>5.11032</mmcif_mdb:model_Cartn_z> <mmcif_mdb:substruct_code>side</mmcif_mdb:substruct_code> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:chem_comp_atom> <mmcif_mdb:chem_comp_atom atom_id="CE2" comp_id="phe"> <mmcif_mdb:model_Cartn_x>1.26137</mmcif_mdb:model_Cartn_x> <mmcif_mdb:model_Cartn_y>0.11613</mmcif_mdb:model_Cartn_y> <mmcif_mdb:model_Cartn_z>4.50975</mmcif_mdb:model_Cartn_z> <mmcif_mdb:substruct_code>side</mmcif_mdb:substruct_code> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:chem_comp_atom> <mmcif_mdb:chem_comp_atom atom_id="CD2" comp_id="phe"> <mmcif_mdb:model_Cartn_x>1.23668</mmcif_mdb:model_Cartn_x> <mmcif_mdb:model_Cartn_y>-0.38351</mmcif_mdb:model_Cartn_y> <mmcif_mdb:model_Cartn_z>3.20288</mmcif_mdb:model_Cartn_z> <mmcif_mdb:substruct_code>side</mmcif_mdb:substruct_code> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:chem_comp_atom> <mmcif_mdb:chem_comp_atom atom_id="N" comp_id="val"> <mmcif_mdb:model_Cartn_x>1.20134</mmcif_mdb:model_Cartn_x> <mmcif_mdb:model_Cartn_y>0.84658</mmcif_mdb:model_Cartn_y> <mmcif_mdb:model_Cartn_z>0.00000</mmcif_mdb:model_Cartn_z> <mmcif_mdb:substruct_code>main</mmcif_mdb:substruct_code> <mmcif_mdb:type_symbol>N</mmcif_mdb:type_symbol> </mmcif_mdb:chem_comp_atom> <mmcif_mdb:chem_comp_atom atom_id="CA" comp_id="val"> <mmcif_mdb:model_Cartn_x>0.00000</mmcif_mdb:model_Cartn_x> <mmcif_mdb:model_Cartn_y>0.00000</mmcif_mdb:model_Cartn_y> <mmcif_mdb:model_Cartn_z>0.00000</mmcif_mdb:model_Cartn_z> <mmcif_mdb:substruct_code>main</mmcif_mdb:substruct_code> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:chem_comp_atom> <mmcif_mdb:chem_comp_atom atom_id="C" comp_id="val"> <mmcif_mdb:model_Cartn_x>-1.25029</mmcif_mdb:model_Cartn_x> <mmcif_mdb:model_Cartn_y>0.88107</mmcif_mdb:model_Cartn_y> <mmcif_mdb:model_Cartn_z>0.00000</mmcif_mdb:model_Cartn_z> <mmcif_mdb:substruct_code>main</mmcif_mdb:substruct_code> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:chem_comp_atom> <mmcif_mdb:chem_comp_atom atom_id="O" comp_id="val"> <mmcif_mdb:model_Cartn_x>-2.18525</mmcif_mdb:model_Cartn_x> <mmcif_mdb:model_Cartn_y>0.66029</mmcif_mdb:model_Cartn_y> <mmcif_mdb:model_Cartn_z>-0.78409</mmcif_mdb:model_Cartn_z> <mmcif_mdb:substruct_code>main</mmcif_mdb:substruct_code> <mmcif_mdb:type_symbol>O</mmcif_mdb:type_symbol> </mmcif_mdb:chem_comp_atom> <mmcif_mdb:chem_comp_atom atom_id="CB" comp_id="val"> <mmcif_mdb:model_Cartn_x>0.05260</mmcif_mdb:model_Cartn_x> <mmcif_mdb:model_Cartn_y>-0.99339</mmcif_mdb:model_Cartn_y> <mmcif_mdb:model_Cartn_z>1.17429</mmcif_mdb:model_Cartn_z> <mmcif_mdb:substruct_code>side</mmcif_mdb:substruct_code> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:chem_comp_atom> <mmcif_mdb:chem_comp_atom atom_id="CG1" comp_id="val"> <mmcif_mdb:model_Cartn_x>-0.13288</mmcif_mdb:model_Cartn_x> <mmcif_mdb:model_Cartn_y>-0.31545</mmcif_mdb:model_Cartn_y> <mmcif_mdb:model_Cartn_z>2.52668</mmcif_mdb:model_Cartn_z> <mmcif_mdb:substruct_code>side</mmcif_mdb:substruct_code> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:chem_comp_atom> <mmcif_mdb:chem_comp_atom atom_id="CG2" comp_id="val"> <mmcif_mdb:model_Cartn_x>-0.94265</mmcif_mdb:model_Cartn_x> <mmcif_mdb:model_Cartn_y>-2.12930</mmcif_mdb:model_Cartn_y> <mmcif_mdb:model_Cartn_z>0.99811</mmcif_mdb:model_Cartn_z> <mmcif_mdb:substruct_code>side</mmcif_mdb:substruct_code> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:chem_comp_atom> </mmcif_mdb:chem_comp_atomCategory> An alternative identifier for the atom. This data item would be used in cases where alternative nomenclatures exist for labelling 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, not to atom sites in the ATOM_SITE list. The standard uncertainty (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, not to atom sites in the ATOM_SITE list. The standard uncertainty (estimated standard deviation) of attribute model_Cartn_y in category chem_comp_atom. The z 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, not to atom sites in the ATOM_SITE list. The standard uncertainty (estimated standard deviation) of attribute model_Cartn_z in category chem_comp_atom. The partial charge assigned to this atom. This data item assigns the atom to a substructure of the component, if appropriate. This data item is a pointer to attribute symbol in category atom_type in the ATOM_TYPE category. 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. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. 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. <mmcif_mdb:chem_comp_bondCategory> <mmcif_mdb:chem_comp_bond atom_id_1="N" atom_id_2="CA" comp_id="phe"> <mmcif_mdb:value_order>sing</mmcif_mdb:value_order> </mmcif_mdb:chem_comp_bond> <mmcif_mdb:chem_comp_bond atom_id_1="CA" atom_id_2="C" comp_id="phe"> <mmcif_mdb:value_order>sing</mmcif_mdb:value_order> </mmcif_mdb:chem_comp_bond> <mmcif_mdb:chem_comp_bond atom_id_1="C" atom_id_2="O" comp_id="phe"> <mmcif_mdb:value_order>doub</mmcif_mdb:value_order> </mmcif_mdb:chem_comp_bond> <mmcif_mdb:chem_comp_bond atom_id_1="CB" atom_id_2="CA" comp_id="phe"> <mmcif_mdb:value_order>sing</mmcif_mdb:value_order> </mmcif_mdb:chem_comp_bond> <mmcif_mdb:chem_comp_bond atom_id_1="CB" atom_id_2="CG" comp_id="phe"> <mmcif_mdb:value_order>sing</mmcif_mdb:value_order> </mmcif_mdb:chem_comp_bond> <mmcif_mdb:chem_comp_bond atom_id_1="CG" atom_id_2="CD1" comp_id="phe"> <mmcif_mdb:value_order>arom</mmcif_mdb:value_order> </mmcif_mdb:chem_comp_bond> <mmcif_mdb:chem_comp_bond atom_id_1="CD1" atom_id_2="CE1" comp_id="phe"> <mmcif_mdb:value_order>arom</mmcif_mdb:value_order> </mmcif_mdb:chem_comp_bond> <mmcif_mdb:chem_comp_bond atom_id_1="CE1" atom_id_2="CZ" comp_id="phe"> <mmcif_mdb:value_order>arom</mmcif_mdb:value_order> </mmcif_mdb:chem_comp_bond> <mmcif_mdb:chem_comp_bond atom_id_1="CZ" atom_id_2="CE2" comp_id="phe"> <mmcif_mdb:value_order>arom</mmcif_mdb:value_order> </mmcif_mdb:chem_comp_bond> <mmcif_mdb:chem_comp_bond atom_id_1="CE2" atom_id_2="CD2" comp_id="phe"> <mmcif_mdb:value_order>arom</mmcif_mdb:value_order> </mmcif_mdb:chem_comp_bond> <mmcif_mdb:chem_comp_bond atom_id_1="CD2" atom_id_2="CG" comp_id="phe"> <mmcif_mdb:value_order>arom</mmcif_mdb:value_order> </mmcif_mdb:chem_comp_bond> <mmcif_mdb:chem_comp_bond atom_id_1="N" atom_id_2="CA" comp_id="val"> <mmcif_mdb:value_order>sing</mmcif_mdb:value_order> </mmcif_mdb:chem_comp_bond> <mmcif_mdb:chem_comp_bond atom_id_1="CA" atom_id_2="C" comp_id="val"> <mmcif_mdb:value_order>sing</mmcif_mdb:value_order> </mmcif_mdb:chem_comp_bond> <mmcif_mdb:chem_comp_bond atom_id_1="C" atom_id_2="O" comp_id="val"> <mmcif_mdb:value_order>doub</mmcif_mdb:value_order> </mmcif_mdb:chem_comp_bond> <mmcif_mdb:chem_comp_bond atom_id_1="CB" atom_id_2="CA" comp_id="val"> <mmcif_mdb:value_order>sing</mmcif_mdb:value_order> </mmcif_mdb:chem_comp_bond> <mmcif_mdb:chem_comp_bond atom_id_1="CB" atom_id_2="CG1" comp_id="val"> <mmcif_mdb:value_order>sing</mmcif_mdb:value_order> </mmcif_mdb:chem_comp_bond> <mmcif_mdb:chem_comp_bond atom_id_1="CB" atom_id_2="CG2" comp_id="val"> <mmcif_mdb:value_order>sing</mmcif_mdb:value_order> </mmcif_mdb:chem_comp_bond> </mmcif_mdb:chem_comp_bondCategory> The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a distance. The standard uncertainty (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. 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. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. Data items in the CHEM_COMP_CHIR category provide details about the chiral centres 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. <mmcif_mdb:chem_comp_chirCategory> <mmcif_mdb:chem_comp_chir comp_id="phe" id="phe1"> <mmcif_mdb:atom_id>CA</mmcif_mdb:atom_id> </mmcif_mdb:chem_comp_chir> <mmcif_mdb:chem_comp_chir comp_id="val" id="val1"> <mmcif_mdb:atom_id>CA</mmcif_mdb:atom_id> </mmcif_mdb:chem_comp_chir> </mmcif_mdb:chem_comp_chirCategory> The chiral configuration of the atom that is a chiral centre. The ID of the atom that is a chiral centre. 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 centres 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 standard uncertainty (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. <mmcif_mdb:chem_comp_chir_atomCategory> <mmcif_mdb:chem_comp_chir_atom atom_id="N" chir_id="1" comp_id="phe"></mmcif_mdb:chem_comp_chir_atom> <mmcif_mdb:chem_comp_chir_atom atom_id="C" chir_id="1" comp_id="phe"></mmcif_mdb:chem_comp_chir_atom> <mmcif_mdb:chem_comp_chir_atom atom_id="CB" chir_id="1" comp_id="phe"></mmcif_mdb:chem_comp_chir_atom> <mmcif_mdb:chem_comp_chir_atom atom_id="N" chir_id="1" comp_id="val"></mmcif_mdb:chem_comp_chir_atom> <mmcif_mdb:chem_comp_chir_atom atom_id="C" chir_id="1" comp_id="val"></mmcif_mdb:chem_comp_chir_atom> <mmcif_mdb:chem_comp_chir_atom atom_id="CB" chir_id="1" comp_id="val"></mmcif_mdb:chem_comp_chir_atom> </mmcif_mdb:chem_comp_chir_atomCategory> The standard uncertainty (estimated standard deviation) of the position of this atom from the plane defined by all of the atoms in the plane. 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_chir in the CHEM_COMP_CHIR 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 links between chemical components. A description of special aspects of a link between chemical components in the structure. The type of the first of the two components joined by the link. 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 link. 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. <mmcif_mdb:chem_comp_planeCategory> <mmcif_mdb:chem_comp_plane comp_id="phe" id="phe1"></mmcif_mdb:chem_comp_plane> </mmcif_mdb: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. <mmcif_mdb:chem_comp_plane_atomCategory> <mmcif_mdb:chem_comp_plane_atom atom_id="CB" comp_id="phe" plane_id="phe1"></mmcif_mdb:chem_comp_plane_atom> <mmcif_mdb:chem_comp_plane_atom atom_id="CG" comp_id="phe" plane_id="phe1"></mmcif_mdb:chem_comp_plane_atom> <mmcif_mdb:chem_comp_plane_atom atom_id="CD1" comp_id="phe" plane_id="phe1"></mmcif_mdb:chem_comp_plane_atom> <mmcif_mdb:chem_comp_plane_atom atom_id="CE1" comp_id="phe" plane_id="phe1"></mmcif_mdb:chem_comp_plane_atom> <mmcif_mdb:chem_comp_plane_atom atom_id="CZ" comp_id="phe" plane_id="phe1"></mmcif_mdb:chem_comp_plane_atom> <mmcif_mdb:chem_comp_plane_atom atom_id="CE2" comp_id="phe" plane_id="phe1"></mmcif_mdb:chem_comp_plane_atom> <mmcif_mdb:chem_comp_plane_atom atom_id="CD2" comp_id="phe" plane_id="phe1"></mmcif_mdb:chem_comp_plane_atom> </mmcif_mdb:chem_comp_plane_atomCategory> This data item is the standard deviation of the out-of-plane distance for this atom. 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. This data item is a pointer to attribute id in category chem_comp_plane in the CHEM_COMP_PLANE 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. <mmcif_mdb:chem_comp_torCategory> <mmcif_mdb:chem_comp_tor comp_id="phe" id="phe_chi1"> <mmcif_mdb:atom_id_1>N</mmcif_mdb:atom_id_1> <mmcif_mdb:atom_id_2>CA</mmcif_mdb:atom_id_2> <mmcif_mdb:atom_id_3>CB</mmcif_mdb:atom_id_3> <mmcif_mdb:atom_id_4>CG</mmcif_mdb:atom_id_4> </mmcif_mdb:chem_comp_tor> <mmcif_mdb:chem_comp_tor comp_id="phe" id="phe_chi2"> <mmcif_mdb:atom_id_1>CA</mmcif_mdb:atom_id_1> <mmcif_mdb:atom_id_2>CB</mmcif_mdb:atom_id_2> <mmcif_mdb:atom_id_3>CG</mmcif_mdb:atom_id_3> <mmcif_mdb:atom_id_4>CD1</mmcif_mdb:atom_id_4> </mmcif_mdb:chem_comp_tor> <mmcif_mdb:chem_comp_tor comp_id="phe" id="phe_ring1"> <mmcif_mdb:atom_id_1>CB</mmcif_mdb:atom_id_1> <mmcif_mdb:atom_id_2>CG</mmcif_mdb:atom_id_2> <mmcif_mdb:atom_id_3>CD1</mmcif_mdb:atom_id_3> <mmcif_mdb:atom_id_4>CE1</mmcif_mdb:atom_id_4> </mmcif_mdb:chem_comp_tor> <mmcif_mdb:chem_comp_tor comp_id="phe" id="phe_ring2"> <mmcif_mdb:atom_id_1>CB</mmcif_mdb:atom_id_1> <mmcif_mdb:atom_id_2>CG</mmcif_mdb:atom_id_2> <mmcif_mdb:atom_id_3>CD2</mmcif_mdb:atom_id_3> <mmcif_mdb:atom_id_4>CE2</mmcif_mdb:atom_id_4> </mmcif_mdb:chem_comp_tor> <mmcif_mdb:chem_comp_tor comp_id="phe" id="phe_ring3"> <mmcif_mdb:atom_id_1>CG</mmcif_mdb:atom_id_1> <mmcif_mdb:atom_id_2>CD1</mmcif_mdb:atom_id_2> <mmcif_mdb:atom_id_3>CE1</mmcif_mdb:atom_id_3> <mmcif_mdb:atom_id_4>CZ</mmcif_mdb:atom_id_4> </mmcif_mdb:chem_comp_tor> <mmcif_mdb:chem_comp_tor comp_id="phe" id="phe_ring4"> <mmcif_mdb:atom_id_1>CD1</mmcif_mdb:atom_id_1> <mmcif_mdb:atom_id_2>CE1</mmcif_mdb:atom_id_2> <mmcif_mdb:atom_id_3>CZ</mmcif_mdb:atom_id_3> <mmcif_mdb:atom_id_4>CE2</mmcif_mdb:atom_id_4> </mmcif_mdb:chem_comp_tor> <mmcif_mdb:chem_comp_tor comp_id="phe" id="phe_ring5"> <mmcif_mdb:atom_id_1>CE1</mmcif_mdb:atom_id_1> <mmcif_mdb:atom_id_2>CZ</mmcif_mdb:atom_id_2> <mmcif_mdb:atom_id_3>CE2</mmcif_mdb:atom_id_3> <mmcif_mdb:atom_id_4>CD2</mmcif_mdb:atom_id_4> </mmcif_mdb:chem_comp_tor> </mmcif_mdb: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. <mmcif_mdb:chem_comp_tor_valueCategory> <mmcif_mdb:chem_comp_tor_value comp_id="phe" tor_id="phe_chi1"> <mmcif_mdb:angle>-60.0</mmcif_mdb:angle> <mmcif_mdb:dist>2.88</mmcif_mdb:dist> </mmcif_mdb:chem_comp_tor_value> <mmcif_mdb:chem_comp_tor_value comp_id="phe" tor_id="phe_chi1"> <mmcif_mdb:angle>180.0</mmcif_mdb:angle> <mmcif_mdb:dist>3.72</mmcif_mdb:dist> </mmcif_mdb:chem_comp_tor_value> <mmcif_mdb:chem_comp_tor_value comp_id="phe" tor_id="phe_chi1"> <mmcif_mdb:angle>60.0</mmcif_mdb:angle> <mmcif_mdb:dist>2.88</mmcif_mdb:dist> </mmcif_mdb:chem_comp_tor_value> <mmcif_mdb:chem_comp_tor_value comp_id="phe" tor_id="phe_chi2"> <mmcif_mdb:angle>90.0</mmcif_mdb:angle> <mmcif_mdb:dist>3.34</mmcif_mdb:dist> </mmcif_mdb:chem_comp_tor_value> <mmcif_mdb:chem_comp_tor_value comp_id="phe" tor_id="phe_chi2"> <mmcif_mdb:angle>-90.0</mmcif_mdb:angle> <mmcif_mdb:dist>3.34</mmcif_mdb:dist> </mmcif_mdb:chem_comp_tor_value> <mmcif_mdb:chem_comp_tor_value comp_id="phe" tor_id="phe_ring1"> <mmcif_mdb:angle>180.0</mmcif_mdb:angle> <mmcif_mdb:dist>3.75</mmcif_mdb:dist> </mmcif_mdb:chem_comp_tor_value> <mmcif_mdb:chem_comp_tor_value comp_id="phe" tor_id="phe_ring2"> <mmcif_mdb:angle>180.0</mmcif_mdb:angle> <mmcif_mdb:dist>3.75</mmcif_mdb:dist> </mmcif_mdb:chem_comp_tor_value> <mmcif_mdb:chem_comp_tor_value comp_id="phe" tor_id="phe_ring3"> <mmcif_mdb:angle>0.0</mmcif_mdb:angle> <mmcif_mdb:dist>2.80</mmcif_mdb:dist> </mmcif_mdb:chem_comp_tor_value> <mmcif_mdb:chem_comp_tor_value comp_id="phe" tor_id="phe_ring4"> <mmcif_mdb:angle>0.0</mmcif_mdb:angle> <mmcif_mdb:dist>2.80</mmcif_mdb:dist> </mmcif_mdb:chem_comp_tor_value> <mmcif_mdb:chem_comp_tor_value comp_id="phe" tor_id="phe_ring5"> <mmcif_mdb:angle>0.0</mmcif_mdb:angle> <mmcif_mdb:dist>2.80</mmcif_mdb:dist> </mmcif_mdb:chem_comp_tor_value> </mmcif_mdb: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 standard uncertainty (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 degree 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 standard uncertainty (estimated standard deviation) of attribute dist in category chem_comp_tor_value. This data item is a pointer to attribute comp_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_tor in the CHEM_COMP_TOR category. Data items in the CHEM_LINK category give details about the links between chemical components. A description of special aspects of a link 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 link between chemical components. Example 1 - Engh & Huber parameters [Acta Cryst. (1991), A47, 392-400] as interpreted by J. P. Priestle (1995). Consistent Stereochemical Dictionaries for Refinement and Model Building. CCP4 Daresbury Study Weekend, DL-CONF-95-001, ISSN 1358-6254. Warrington: Daresbury Laboratory. <mmcif_mdb:chem_link_angleCategory> <mmcif_mdb:chem_link_angle atom_id_1="N" atom_id_2="CA" atom_id_3="C" link_id="PEPTIDE"> <mmcif_mdb:atom_1_comp_id>1</mmcif_mdb:atom_1_comp_id> <mmcif_mdb:atom_2_comp_id>1</mmcif_mdb:atom_2_comp_id> <mmcif_mdb:atom_3_comp_id>1</mmcif_mdb:atom_3_comp_id> <mmcif_mdb:value_angle>111.2</mmcif_mdb:value_angle> <mmcif_mdb:value_angle_esd>2.8</mmcif_mdb:value_angle_esd> </mmcif_mdb:chem_link_angle> <mmcif_mdb:chem_link_angle atom_id_1="CA" atom_id_2="C" atom_id_3="O" link_id="PEPTIDE"> <mmcif_mdb:atom_1_comp_id>1</mmcif_mdb:atom_1_comp_id> <mmcif_mdb:atom_2_comp_id>1</mmcif_mdb:atom_2_comp_id> <mmcif_mdb:atom_3_comp_id>1</mmcif_mdb:atom_3_comp_id> <mmcif_mdb:value_angle>120.8</mmcif_mdb:value_angle> <mmcif_mdb:value_angle_esd>1.7</mmcif_mdb:value_angle_esd> </mmcif_mdb:chem_link_angle> <mmcif_mdb:chem_link_angle atom_id_1="CA" atom_id_2="C" atom_id_3="N" link_id="PEPTIDE"> <mmcif_mdb:atom_1_comp_id>1</mmcif_mdb:atom_1_comp_id> <mmcif_mdb:atom_2_comp_id>1</mmcif_mdb:atom_2_comp_id> <mmcif_mdb:atom_3_comp_id>2</mmcif_mdb:atom_3_comp_id> <mmcif_mdb:value_angle>116.2</mmcif_mdb:value_angle> <mmcif_mdb:value_angle_esd>2.0</mmcif_mdb:value_angle_esd> </mmcif_mdb:chem_link_angle> <mmcif_mdb:chem_link_angle atom_id_1="O" atom_id_2="C" atom_id_3="N" link_id="PEPTIDE"> <mmcif_mdb:atom_1_comp_id>1</mmcif_mdb:atom_1_comp_id> <mmcif_mdb:atom_2_comp_id>1</mmcif_mdb:atom_2_comp_id> <mmcif_mdb:atom_3_comp_id>2</mmcif_mdb:atom_3_comp_id> <mmcif_mdb:value_angle>123.0</mmcif_mdb:value_angle> <mmcif_mdb:value_angle_esd>1.6</mmcif_mdb:value_angle_esd> </mmcif_mdb:chem_link_angle> <mmcif_mdb:chem_link_angle atom_id_1="C" atom_id_2="N" atom_id_3="CA" link_id="PEPTIDE"> <mmcif_mdb:atom_1_comp_id>1</mmcif_mdb:atom_1_comp_id> <mmcif_mdb:atom_2_comp_id>2</mmcif_mdb:atom_2_comp_id> <mmcif_mdb:atom_3_comp_id>2</mmcif_mdb:atom_3_comp_id> <mmcif_mdb:value_angle>121.7</mmcif_mdb:value_angle> <mmcif_mdb:value_angle_esd>1.8</mmcif_mdb:value_angle_esd> </mmcif_mdb:chem_link_angle> </mmcif_mdb: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 link. This data item indicates whether atom 2 is found in the first or the second of the two components connected by the link. This data item indicates whether atom 3 is found in the first or the second of the two components connected by the link. The value that should be taken as the target value for the angle associated with the specified atoms, expressed in degrees. The standard uncertainty (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 standard uncertainty (estimated standard deviation) of attribute value_dist in category chem_comp_angle. 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 attribute type_comp_1 in category chem_comp_link (or attribute type_comp_2 in category chem_comp_link, where the appropriate data item is indicated by the value of attribute atom_1_comp_id) in category chem_comp_angle. 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 attribute type_comp_1 in category chem_comp_link (or attribute type_comp_2 in category chem_comp_link, where the appropriate data item is indicated by the value of attribute atom_2_comp_id) in category chem_comp_angle. 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 attribute type_comp_1 in category chem_comp_link (or attribute type_comp_2 in category chem_comp_link, where the appropriate data item is indicated by the value of attribute atom_3_comp_id) in category chem_comp_angle. This data item is a pointer to attribute id in category chem_link in the CHEM_LINK category. Data items in the CHEM_LINK_BOND category record details about bonds in a link between components in the chemical structure. Example 1 - Engh & Huber parameters [Acta Cryst. (1991), A47, 392-400] as interpreted by J. P. Priestle (1995). Consistent Stereochemical Dictionaries for Refinement and Model Building. CCP4 Daresbury Study Weekend, DL-CONF-95-001, ISSN 1358-6254. Warrington: Daresbury Laboratory. <mmcif_mdb:chem_link_bondCategory> <mmcif_mdb:chem_link_bond atom_id_1="N" atom_id_2="CA" link_id="PEPTIDE"> <mmcif_mdb:atom_1_comp_id>1</mmcif_mdb:atom_1_comp_id> <mmcif_mdb:atom_2_comp_id>1</mmcif_mdb:atom_2_comp_id> <mmcif_mdb:value_dist>1.458</mmcif_mdb:value_dist> <mmcif_mdb:value_dist_esd>0.019</mmcif_mdb:value_dist_esd> </mmcif_mdb:chem_link_bond> <mmcif_mdb:chem_link_bond atom_id_1="CA" atom_id_2="C" link_id="PEPTIDE"> <mmcif_mdb:atom_1_comp_id>1</mmcif_mdb:atom_1_comp_id> <mmcif_mdb:atom_2_comp_id>1</mmcif_mdb:atom_2_comp_id> <mmcif_mdb:value_dist>1.525</mmcif_mdb:value_dist> <mmcif_mdb:value_dist_esd>0.021</mmcif_mdb:value_dist_esd> </mmcif_mdb:chem_link_bond> <mmcif_mdb:chem_link_bond atom_id_1="C" atom_id_2="N" link_id="PEPTIDE"> <mmcif_mdb:atom_1_comp_id>1</mmcif_mdb:atom_1_comp_id> <mmcif_mdb:atom_2_comp_id>2</mmcif_mdb:atom_2_comp_id> <mmcif_mdb:value_dist>1.329</mmcif_mdb:value_dist> <mmcif_mdb:value_dist_esd>0.014</mmcif_mdb:value_dist_esd> </mmcif_mdb:chem_link_bond> <mmcif_mdb:chem_link_bond atom_id_1="C" atom_id_2="O" link_id="PEPTIDE"> <mmcif_mdb:atom_1_comp_id>1</mmcif_mdb:atom_1_comp_id> <mmcif_mdb:atom_2_comp_id>1</mmcif_mdb:atom_2_comp_id> <mmcif_mdb:value_dist>1.231</mmcif_mdb:value_dist> <mmcif_mdb:value_dist_esd>0.020</mmcif_mdb:value_dist_esd> </mmcif_mdb:chem_link_bond> </mmcif_mdb: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 link. This data item indicates whether atom 2 is found in the first or the second of the two chemical components connected by the link. The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a distance. The standard uncertainty (estimated standard deviation) of attribute value_dist 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. 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. This data item is a pointer to attribute id in category chem_link in the CHEM_LINK category. Data items in the CHEM_LINK_CHIR category provide details about the chiral centres in a link between two chemical components. The atoms bonded to the chiral atom are specified in the CHEM_LINK_CHIR_ATOM category. This data item indicates whether the chiral atom is found in the first or the second of the two components connected by the link. The chiral configuration of the atom that is a chiral centre. The ID of the atom that is a chiral centre. 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 centres 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 standard uncertainty (estimated standard deviation) of attribute volume_three in category chem_link_chir. The value of attribute id in category chem_link_chir must uniquely identify a record in the CHEM_LINK_CHIR list. This data item is a pointer to attribute id in category chem_link in the CHEM_LINK category. Data items in the CHEM_LINK_CHIR_ATOM category enumerate the atoms bonded to a chiral atom in a link between two chemical components. 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 link. The standard uncertainty (estimated standard deviation) of the position of this atom from the plane defined by all of the atoms in the plane. 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. This data item is a pointer to attribute id in category chem_link_chir in the CHEM_LINK_CHIR category. Data items in the CHEM_LINK_PLANE category provide identifiers for the planes in a link between two chemical components. The atoms in the plane are specified in the CHEM_LINK_PLANE_ATOM category. The total number of atoms in the plane. The number of non-hydrogen atoms in the plane. The value of attribute id in category chem_link_plane must uniquely identify a record in the CHEM_LINK_PLANE list. This data item is a pointer to attribute id in category chem_link in the CHEM_LINK category. Data items in the CHEM_LINK_PLANE_ATOM category enumerate the atoms in a plane in a link between two chemical components. 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 link. 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. This data item is a pointer to attribute id in category chem_link_plane in the CHEM_LINK_PLANE category. Data items in the CHEM_LINK_TOR category record details about the torsion angles in a link 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. This data item indicates whether atom 1 is found in the first or the second of the two components connected by the link. This data item indicates whether atom 2 is found in the first or the second of the two components connected by the link. This data item indicates whether atom 3 is found in the first or the second of the two components connected by the link. This data item indicates whether atom 4 is found in the first or the second of the two components connected by the link. 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. The value of attribute id in category chem_link_tor must uniquely identify a record in the CHEM_LINK_TOR list. This data item is a pointer to attribute id in category chem_link in the CHEM_LINK category. 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. A value that should be taken as a potential target value for the torsion angle associated with the specified atoms, expressed in degrees. The standard uncertainty (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 degree 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 standard uncertainty (estimated standard deviation) of attribute dist 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 [Acta Cryst. (1996), C52, 765-767]. <mmcif_mdb:chemicalCategory> <mmcif_mdb:chemical entry_id="9597gaus"> <mmcif_mdb:name_systematic>trans-bis(tricyclohexylphosphine)tetracarbonylmolybdenum(0)</mmcif_mdb:name_systematic> </mmcif_mdb:chemical> </mmcif_mdb: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 the 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 the 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 two-dimensional (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 [Acta Cryst. (1996), C52, 951-953]. <mmcif_mdb:chemical_conn_atomCategory> <mmcif_mdb:chemical_conn_atom number="1"> <mmcif_mdb:NCA>1</mmcif_mdb:NCA> <mmcif_mdb:NH>0</mmcif_mdb:NH> <mmcif_mdb:display_x>.39</mmcif_mdb:display_x> <mmcif_mdb:display_y>.81</mmcif_mdb:display_y> <mmcif_mdb:type_symbol>S</mmcif_mdb:type_symbol> </mmcif_mdb:chemical_conn_atom> <mmcif_mdb:chemical_conn_atom number="2"> <mmcif_mdb:NCA>2</mmcif_mdb:NCA> <mmcif_mdb:NH>0</mmcif_mdb:NH> <mmcif_mdb:display_x>.39</mmcif_mdb:display_x> <mmcif_mdb:display_y>.96</mmcif_mdb:display_y> <mmcif_mdb:type_symbol>S</mmcif_mdb:type_symbol> </mmcif_mdb:chemical_conn_atom> <mmcif_mdb:chemical_conn_atom number="3"> <mmcif_mdb:NCA>3</mmcif_mdb:NCA> <mmcif_mdb:NH>0</mmcif_mdb:NH> <mmcif_mdb:display_x>.14</mmcif_mdb:display_x> <mmcif_mdb:display_y>.88</mmcif_mdb:display_y> <mmcif_mdb:type_symbol>N</mmcif_mdb:type_symbol> </mmcif_mdb:chemical_conn_atom> <mmcif_mdb:chemical_conn_atom number="4"> <mmcif_mdb:NCA>3</mmcif_mdb:NCA> <mmcif_mdb:NH>0</mmcif_mdb:NH> <mmcif_mdb:display_x>.33</mmcif_mdb:display_x> <mmcif_mdb:display_y>.88</mmcif_mdb:display_y> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:chemical_conn_atom> <mmcif_mdb:chemical_conn_atom number="5"> <mmcif_mdb:NCA>2</mmcif_mdb:NCA> <mmcif_mdb:NH>2</mmcif_mdb:NH> <mmcif_mdb:display_x>.11</mmcif_mdb:display_x> <mmcif_mdb:display_y>.96</mmcif_mdb:display_y> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:chemical_conn_atom> <mmcif_mdb:chemical_conn_atom number="6"> <mmcif_mdb:NCA>2</mmcif_mdb:NCA> <mmcif_mdb:NH>2</mmcif_mdb:NH> <mmcif_mdb:display_x>.03</mmcif_mdb:display_x> <mmcif_mdb:display_y>.96</mmcif_mdb:display_y> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:chemical_conn_atom> <mmcif_mdb:chemical_conn_atom number="7"> <mmcif_mdb:NCA>2</mmcif_mdb:NCA> <mmcif_mdb:NH>2</mmcif_mdb:NH> <mmcif_mdb:display_x>.03</mmcif_mdb:display_x> <mmcif_mdb:display_y>.80</mmcif_mdb:display_y> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:chemical_conn_atom> <mmcif_mdb:chemical_conn_atom number="8"> <mmcif_mdb:NCA>2</mmcif_mdb:NCA> <mmcif_mdb:NH>2</mmcif_mdb:NH> <mmcif_mdb:display_x>.11</mmcif_mdb:display_x> <mmcif_mdb:display_y>.80</mmcif_mdb:display_y> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:chemical_conn_atom> <mmcif_mdb:chemical_conn_atom number="9"> <mmcif_mdb:NCA>1</mmcif_mdb:NCA> <mmcif_mdb:NH>0</mmcif_mdb:NH> <mmcif_mdb:display_x>.54</mmcif_mdb:display_x> <mmcif_mdb:display_y>.81</mmcif_mdb:display_y> <mmcif_mdb:type_symbol>S</mmcif_mdb:type_symbol> </mmcif_mdb:chemical_conn_atom> <mmcif_mdb:chemical_conn_atom number="10"> <mmcif_mdb:NCA>2</mmcif_mdb:NCA> <mmcif_mdb:NH>0</mmcif_mdb:NH> <mmcif_mdb:display_x>.54</mmcif_mdb:display_x> <mmcif_mdb:display_y>.96</mmcif_mdb:display_y> <mmcif_mdb:type_symbol>S</mmcif_mdb:type_symbol> </mmcif_mdb:chemical_conn_atom> <mmcif_mdb:chemical_conn_atom number="11"> <mmcif_mdb:NCA>3</mmcif_mdb:NCA> <mmcif_mdb:NH>0</mmcif_mdb:NH> <mmcif_mdb:display_x>.80</mmcif_mdb:display_x> <mmcif_mdb:display_y>.88</mmcif_mdb:display_y> <mmcif_mdb:type_symbol>N</mmcif_mdb:type_symbol> </mmcif_mdb:chemical_conn_atom> <mmcif_mdb:chemical_conn_atom number="12"> <mmcif_mdb:NCA>3</mmcif_mdb:NCA> <mmcif_mdb:NH>0</mmcif_mdb:NH> <mmcif_mdb:display_x>.60</mmcif_mdb:display_x> <mmcif_mdb:display_y>.88</mmcif_mdb:display_y> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:chemical_conn_atom> <mmcif_mdb:chemical_conn_atom number="13"> <mmcif_mdb:NCA>2</mmcif_mdb:NCA> <mmcif_mdb:NH>2</mmcif_mdb:NH> <mmcif_mdb:display_x>.84</mmcif_mdb:display_x> <mmcif_mdb:display_y>.96</mmcif_mdb:display_y> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:chemical_conn_atom> <mmcif_mdb:chemical_conn_atom number="14"> <mmcif_mdb:NCA>2</mmcif_mdb:NCA> <mmcif_mdb:NH>2</mmcif_mdb:NH> <mmcif_mdb:display_x>.91</mmcif_mdb:display_x> <mmcif_mdb:display_y>.96</mmcif_mdb:display_y> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:chemical_conn_atom> <mmcif_mdb:chemical_conn_atom number="15"> <mmcif_mdb:NCA>2</mmcif_mdb:NCA> <mmcif_mdb:NH>2</mmcif_mdb:NH> <mmcif_mdb:display_x>.91</mmcif_mdb:display_x> <mmcif_mdb:display_y>.80</mmcif_mdb:display_y> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:chemical_conn_atom> <mmcif_mdb:chemical_conn_atom number="16"> <mmcif_mdb:NCA>2</mmcif_mdb:NCA> <mmcif_mdb:NH>2</mmcif_mdb:NH> <mmcif_mdb:display_x>.84</mmcif_mdb:display_x> <mmcif_mdb:display_y>.80</mmcif_mdb:display_y> <mmcif_mdb:type_symbol>C</mmcif_mdb:type_symbol> </mmcif_mdb:chemical_conn_atom> </mmcif_mdb: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 recognizable 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. The 2D Cartesian y coordinate of the position of this atom in a recognizable 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. 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 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 two-dimensional (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 [Acta Cryst. (1996), C52, 951-953]. <mmcif_mdb:chemical_conn_bondCategory> <mmcif_mdb:chemical_conn_bond atom_1="4" atom_2="1"> <mmcif_mdb:type>doub</mmcif_mdb:type> </mmcif_mdb:chemical_conn_bond> <mmcif_mdb:chemical_conn_bond atom_1="4" atom_2="3"> <mmcif_mdb:type>sing</mmcif_mdb:type> </mmcif_mdb:chemical_conn_bond> <mmcif_mdb:chemical_conn_bond atom_1="4" atom_2="2"> <mmcif_mdb:type>sing</mmcif_mdb:type> </mmcif_mdb:chemical_conn_bond> <mmcif_mdb:chemical_conn_bond atom_1="5" atom_2="3"> <mmcif_mdb:type>sing</mmcif_mdb:type> </mmcif_mdb:chemical_conn_bond> <mmcif_mdb:chemical_conn_bond atom_1="6" atom_2="5"> <mmcif_mdb:type>sing</mmcif_mdb:type> </mmcif_mdb:chemical_conn_bond> <mmcif_mdb:chemical_conn_bond atom_1="7" atom_2="6"> <mmcif_mdb:type>sing</mmcif_mdb:type> </mmcif_mdb:chemical_conn_bond> <mmcif_mdb:chemical_conn_bond atom_1="8" atom_2="7"> <mmcif_mdb:type>sing</mmcif_mdb:type> </mmcif_mdb:chemical_conn_bond> <mmcif_mdb:chemical_conn_bond atom_1="8" atom_2="3"> <mmcif_mdb:type>sing</mmcif_mdb:type> </mmcif_mdb:chemical_conn_bond> <mmcif_mdb:chemical_conn_bond atom_1="10" atom_2="2"> <mmcif_mdb:type>sing</mmcif_mdb:type> </mmcif_mdb:chemical_conn_bond> <mmcif_mdb:chemical_conn_bond atom_1="12" atom_2="9"> <mmcif_mdb:type>doub</mmcif_mdb:type> </mmcif_mdb:chemical_conn_bond> <mmcif_mdb:chemical_conn_bond atom_1="12" atom_2="11"> <mmcif_mdb:type>sing</mmcif_mdb:type> </mmcif_mdb:chemical_conn_bond> <mmcif_mdb:chemical_conn_bond atom_1="12" atom_2="10"> <mmcif_mdb:type>sing</mmcif_mdb:type> </mmcif_mdb:chemical_conn_bond> <mmcif_mdb:chemical_conn_bond atom_1="13" atom_2="11"> <mmcif_mdb:type>sing</mmcif_mdb:type> </mmcif_mdb:chemical_conn_bond> <mmcif_mdb:chemical_conn_bond atom_1="14" atom_2="13"> <mmcif_mdb:type>sing</mmcif_mdb:type> </mmcif_mdb:chemical_conn_bond> <mmcif_mdb:chemical_conn_bond atom_1="15" atom_2="14"> <mmcif_mdb:type>sing</mmcif_mdb:type> </mmcif_mdb:chemical_conn_bond> <mmcif_mdb:chemical_conn_bond atom_1="16" atom_2="15"> <mmcif_mdb:type>sing</mmcif_mdb:type> </mmcif_mdb:chemical_conn_bond> <mmcif_mdb:chemical_conn_bond atom_1="16" atom_2="11"> <mmcif_mdb:type>sing</mmcif_mdb:type> </mmcif_mdb:chemical_conn_bond> <mmcif_mdb:chemical_conn_bond atom_1="17" atom_2="5"> <mmcif_mdb:type>sing</mmcif_mdb:type> </mmcif_mdb:chemical_conn_bond> <mmcif_mdb:chemical_conn_bond atom_1="18" atom_2="5"> <mmcif_mdb:type>sing</mmcif_mdb:type> </mmcif_mdb:chemical_conn_bond> <mmcif_mdb:chemical_conn_bond atom_1="19" atom_2="6"> <mmcif_mdb:type>sing</mmcif_mdb:type> </mmcif_mdb:chemical_conn_bond> <mmcif_mdb:chemical_conn_bond atom_1="20" atom_2="6"> <mmcif_mdb:type>sing</mmcif_mdb:type> </mmcif_mdb:chemical_conn_bond> <mmcif_mdb:chemical_conn_bond atom_1="21" atom_2="7"> <mmcif_mdb:type>sing</mmcif_mdb:type> </mmcif_mdb:chemical_conn_bond> <mmcif_mdb:chemical_conn_bond atom_1="22" atom_2="7"> <mmcif_mdb:type>sing</mmcif_mdb:type> </mmcif_mdb:chemical_conn_bond> <mmcif_mdb:chemical_conn_bond atom_1="23" atom_2="8"> <mmcif_mdb:type>sing</mmcif_mdb:type> </mmcif_mdb:chemical_conn_bond> <mmcif_mdb:chemical_conn_bond atom_1="24" atom_2="8"> <mmcif_mdb:type>sing</mmcif_mdb:type> </mmcif_mdb:chemical_conn_bond> <mmcif_mdb:chemical_conn_bond atom_1="25" atom_2="13"> <mmcif_mdb:type>sing</mmcif_mdb:type> </mmcif_mdb:chemical_conn_bond> <mmcif_mdb:chemical_conn_bond atom_1="26" atom_2="13"> <mmcif_mdb:type>sing</mmcif_mdb:type> </mmcif_mdb:chemical_conn_bond> <mmcif_mdb:chemical_conn_bond atom_1="27" atom_2="14"> <mmcif_mdb:type>sing</mmcif_mdb:type> </mmcif_mdb:chemical_conn_bond> <mmcif_mdb:chemical_conn_bond atom_1="28" atom_2="14"> <mmcif_mdb:type>sing</mmcif_mdb:type> </mmcif_mdb:chemical_conn_bond> <mmcif_mdb:chemical_conn_bond atom_1="29" atom_2="15"> <mmcif_mdb:type>sing</mmcif_mdb:type> </mmcif_mdb:chemical_conn_bond> <mmcif_mdb:chemical_conn_bond atom_1="30" atom_2="15"> <mmcif_mdb:type>sing</mmcif_mdb:type> </mmcif_mdb:chemical_conn_bond> <mmcif_mdb:chemical_conn_bond atom_1="31" atom_2="16"> <mmcif_mdb:type>sing</mmcif_mdb:type> </mmcif_mdb:chemical_conn_bond> <mmcif_mdb:chemical_conn_bond atom_1="32" atom_2="16"> <mmcif_mdb:type>sing</mmcif_mdb:type> </mmcif_mdb:chemical_conn_bond> </mmcif_mdb: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 recognized 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 parenthesis. 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, then H, then 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]. <mmcif_mdb:chemical_formulaCategory> <mmcif_mdb:chemical_formula entry_id="TOZ"> <mmcif_mdb:moiety>C18 H25 N O3</mmcif_mdb:moiety> <mmcif_mdb:sum>C18 H25 N O3</mmcif_mdb:sum> <mmcif_mdb:weight>303.40</mmcif_mdb:weight> </mmcif_mdb:chemical_formula> </mmcif_mdb: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 (estimated standard deviations). 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_FORMULA 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 _chemical_formula.sum 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 as being 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. <mmcif_mdb:citationCategory> <mmcif_mdb:citation id="primary"> <mmcif_mdb:book_id_ISBN></mmcif_mdb:book_id_ISBN> <mmcif_mdb:book_publisher></mmcif_mdb:book_publisher> <mmcif_mdb:book_title></mmcif_mdb:book_title> <mmcif_mdb:coordinate_linkage>yes</mmcif_mdb:coordinate_linkage> <mmcif_mdb:country>US</mmcif_mdb:country> <mmcif_mdb:details> The publication that directly relates to this coordinate set.</mmcif_mdb:details> <mmcif_mdb:journal_abbrev>J. Biol. Chem.</mmcif_mdb:journal_abbrev> <mmcif_mdb:journal_id_ASTM>HBCHA3</mmcif_mdb:journal_id_ASTM> <mmcif_mdb:journal_id_CSD>071</mmcif_mdb:journal_id_CSD> <mmcif_mdb:journal_id_ISSN>0021-9258</mmcif_mdb:journal_id_ISSN> <mmcif_mdb:journal_issue></mmcif_mdb:journal_issue> <mmcif_mdb:journal_volume>265</mmcif_mdb:journal_volume> <mmcif_mdb:page_first>14209</mmcif_mdb:page_first> <mmcif_mdb:page_last>14219</mmcif_mdb:page_last> <mmcif_mdb:title> Crystallographic analysis of a complex between human immunodeficiency virus type 1 protease and acetyl-pepstatin at 2.0-Angstroms resolution.</mmcif_mdb:title> <mmcif_mdb:year>1990</mmcif_mdb:year> </mmcif_mdb:citation> <mmcif_mdb:citation id="2"> <mmcif_mdb:book_id_ISBN></mmcif_mdb:book_id_ISBN> <mmcif_mdb:book_publisher></mmcif_mdb:book_publisher> <mmcif_mdb:book_title></mmcif_mdb:book_title> <mmcif_mdb:coordinate_linkage>no</mmcif_mdb:coordinate_linkage> <mmcif_mdb:country>UK</mmcif_mdb:country> <mmcif_mdb:details> Determination of the structure of the unliganded enzyme.</mmcif_mdb:details> <mmcif_mdb:journal_abbrev>Nature</mmcif_mdb:journal_abbrev> <mmcif_mdb:journal_id_ASTM>NATUAS</mmcif_mdb:journal_id_ASTM> <mmcif_mdb:journal_id_CSD>006</mmcif_mdb:journal_id_CSD> <mmcif_mdb:journal_id_ISSN>0028-0836</mmcif_mdb:journal_id_ISSN> <mmcif_mdb:journal_issue></mmcif_mdb:journal_issue> <mmcif_mdb:journal_volume>337</mmcif_mdb:journal_volume> <mmcif_mdb:page_first>615</mmcif_mdb:page_first> <mmcif_mdb:page_last>619</mmcif_mdb:page_last> <mmcif_mdb:title> Three-dimensional structure of aspartyl-protease from human immunodeficiency virus HIV-1.</mmcif_mdb:title> <mmcif_mdb:year>1989</mmcif_mdb:year> </mmcif_mdb:citation> <mmcif_mdb:citation id="3"> <mmcif_mdb:book_id_ISBN></mmcif_mdb:book_id_ISBN> <mmcif_mdb:book_publisher></mmcif_mdb:book_publisher> <mmcif_mdb:book_title></mmcif_mdb:book_title> <mmcif_mdb:coordinate_linkage>no</mmcif_mdb:coordinate_linkage> <mmcif_mdb:country>US</mmcif_mdb:country> <mmcif_mdb:details> Crystallization of the unliganded enzyme.</mmcif_mdb:details> <mmcif_mdb:journal_abbrev>J. Biol. Chem.</mmcif_mdb:journal_abbrev> <mmcif_mdb:journal_id_ASTM>HBCHA3</mmcif_mdb:journal_id_ASTM> <mmcif_mdb:journal_id_CSD>071</mmcif_mdb:journal_id_CSD> <mmcif_mdb:journal_id_ISSN>0021-9258</mmcif_mdb:journal_id_ISSN> <mmcif_mdb:journal_issue></mmcif_mdb:journal_issue> <mmcif_mdb:journal_volume>264</mmcif_mdb:journal_volume> <mmcif_mdb:page_first>1919</mmcif_mdb:page_first> <mmcif_mdb:page_last>1921</mmcif_mdb:page_last> <mmcif_mdb:title> Crystallization of the aspartylprotease from human immunodeficiency virus, HIV-1.</mmcif_mdb:title> <mmcif_mdb:year>1989</mmcif_mdb:year> </mmcif_mdb:citation> <mmcif_mdb:citation id="4"> <mmcif_mdb:book_id_ISBN></mmcif_mdb:book_id_ISBN> <mmcif_mdb:book_publisher></mmcif_mdb:book_publisher> <mmcif_mdb:book_title></mmcif_mdb:book_title> <mmcif_mdb:coordinate_linkage>no</mmcif_mdb:coordinate_linkage> <mmcif_mdb:country>US</mmcif_mdb:country> <mmcif_mdb:details> Expression and purification of the enzyme.</mmcif_mdb:details> <mmcif_mdb:journal_abbrev>J. Biol. Chem.</mmcif_mdb:journal_abbrev> <mmcif_mdb:journal_id_ASTM>HBCHA3</mmcif_mdb:journal_id_ASTM> <mmcif_mdb:journal_id_CSD>071</mmcif_mdb:journal_id_CSD> <mmcif_mdb:journal_id_ISSN>0021-9258</mmcif_mdb:journal_id_ISSN> <mmcif_mdb:journal_issue></mmcif_mdb:journal_issue> <mmcif_mdb:journal_volume>264</mmcif_mdb:journal_volume> <mmcif_mdb:page_first>2307</mmcif_mdb:page_first> <mmcif_mdb:page_last>2312</mmcif_mdb:page_last> <mmcif_mdb:title> Human immunodeficiency virus protease. Bacterial expression and characterization of the purified aspartic protease.</mmcif_mdb:title> <mmcif_mdb:year>1989</mmcif_mdb:year> </mmcif_mdb:citation> </mmcif_mdb: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 books or book chapters. The name of the publisher of the citation; relevant for books or book chapters. John Wiley and Sons The location of the publisher of the citation; relevant for books or book chapters. London The title of the book in which the citation appeared; relevant for books or book chapters. attribute coordinate_linkage in category citation states whether 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 the creation of the data block, the value of this data item would be 'no'. The country of publication; relevant for books and book chapters. Accession number used by Medline to categorize a specific bibliographic entry. 89064067 A description of special aspects of 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 cited journal as given in the Chemical Abstracts Service Source Index. J. Mol. Biol. Full name of the cited journal; relevant for journal articles. Journal of Molecular Biology The American Society for Testing and 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 Protein Data Bank (PDB). 0070 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 cited article is written. German The first page of the citation; relevant for journal articles, books and book chapters. The last page of the citation; relevant for journal articles, books and book chapters. The title of the citation; relevant for journal articles, books and book chapters. Structure of diferric duck ovotransferrin at 2.35 \%A resolution. The year of the citation; relevant for journal articles, books 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 laboratory records for the structure corresponding to PDB entry 5HVP. <mmcif_mdb:citation_authorCategory> <mmcif_mdb:citation_author citation_id="primary" name="Fitzgerald, P.M.D."> <mmcif_mdb:ordinal>1</mmcif_mdb:ordinal> </mmcif_mdb:citation_author> <mmcif_mdb:citation_author citation_id="primary" name="McKeever, B.M."> <mmcif_mdb:ordinal>2</mmcif_mdb:ordinal> </mmcif_mdb:citation_author> <mmcif_mdb:citation_author citation_id="primary" name="Van Middlesworth, J.F."> <mmcif_mdb:ordinal>3</mmcif_mdb:ordinal> </mmcif_mdb:citation_author> <mmcif_mdb:citation_author citation_id="primary" name="Springer, J.P."> <mmcif_mdb:ordinal>4</mmcif_mdb:ordinal> </mmcif_mdb:citation_author> <mmcif_mdb:citation_author citation_id="primary" name="Heimbach, J.C."> <mmcif_mdb:ordinal>5</mmcif_mdb:ordinal> </mmcif_mdb:citation_author> <mmcif_mdb:citation_author citation_id="primary" name="Leu, C.-T."> <mmcif_mdb:ordinal>6</mmcif_mdb:ordinal> </mmcif_mdb:citation_author> <mmcif_mdb:citation_author citation_id="primary" name="Herber, W.K."> <mmcif_mdb:ordinal>7</mmcif_mdb:ordinal> </mmcif_mdb:citation_author> <mmcif_mdb:citation_author citation_id="primary" name="Dixon, R.A.F."> <mmcif_mdb:ordinal>8</mmcif_mdb:ordinal> </mmcif_mdb:citation_author> <mmcif_mdb:citation_author citation_id="primary" name="Darke, P.L."> <mmcif_mdb:ordinal>9</mmcif_mdb:ordinal> </mmcif_mdb:citation_author> <mmcif_mdb:citation_author citation_id="2" name="Navia, M.A."> <mmcif_mdb:ordinal>1</mmcif_mdb:ordinal> </mmcif_mdb:citation_author> <mmcif_mdb:citation_author citation_id="2" name="Fitzgerald, P.M.D."> <mmcif_mdb:ordinal>2</mmcif_mdb:ordinal> </mmcif_mdb:citation_author> <mmcif_mdb:citation_author citation_id="2" name="McKeever, B.M."> <mmcif_mdb:ordinal>3</mmcif_mdb:ordinal> </mmcif_mdb:citation_author> <mmcif_mdb:citation_author citation_id="2" name="Leu, C.-T."> <mmcif_mdb:ordinal>4</mmcif_mdb:ordinal> </mmcif_mdb:citation_author> <mmcif_mdb:citation_author citation_id="2" name="Heimbach, J.C."> <mmcif_mdb:ordinal>5</mmcif_mdb:ordinal> </mmcif_mdb:citation_author> <mmcif_mdb:citation_author citation_id="2" name="Herber, W.K."> <mmcif_mdb:ordinal>6</mmcif_mdb:ordinal> </mmcif_mdb:citation_author> <mmcif_mdb:citation_author citation_id="2" name="Sigal, I.S."> <mmcif_mdb:ordinal>7</mmcif_mdb:ordinal> </mmcif_mdb:citation_author> <mmcif_mdb:citation_author citation_id="2" name="Darke, P.L."> <mmcif_mdb:ordinal>8</mmcif_mdb:ordinal> </mmcif_mdb:citation_author> <mmcif_mdb:citation_author citation_id="2" name="Springer, J.P."> <mmcif_mdb:ordinal>9</mmcif_mdb:ordinal> </mmcif_mdb:citation_author> <mmcif_mdb:citation_author citation_id="3" name="McKeever, B.M."> <mmcif_mdb:ordinal>1</mmcif_mdb:ordinal> </mmcif_mdb:citation_author> <mmcif_mdb:citation_author citation_id="3" name="Navia, M.A."> <mmcif_mdb:ordinal>2</mmcif_mdb:ordinal> </mmcif_mdb:citation_author> <mmcif_mdb:citation_author citation_id="3" name="Fitzgerald, P.M.D."> <mmcif_mdb:ordinal>3</mmcif_mdb:ordinal> </mmcif_mdb:citation_author> <mmcif_mdb:citation_author citation_id="3" name="Springer, J.P."> <mmcif_mdb:ordinal>4</mmcif_mdb:ordinal> </mmcif_mdb:citation_author> <mmcif_mdb:citation_author citation_id="3" name="Leu, C.-T."> <mmcif_mdb:ordinal>5</mmcif_mdb:ordinal> </mmcif_mdb:citation_author> <mmcif_mdb:citation_author citation_id="3" name="Heimbach, J.C."> <mmcif_mdb:ordinal>6</mmcif_mdb:ordinal> </mmcif_mdb:citation_author> <mmcif_mdb:citation_author citation_id="3" name="Herber, W.K."> <mmcif_mdb:ordinal>7</mmcif_mdb:ordinal> </mmcif_mdb:citation_author> <mmcif_mdb:citation_author citation_id="3" name="Sigal, I.S."> <mmcif_mdb:ordinal>8</mmcif_mdb:ordinal> </mmcif_mdb:citation_author> <mmcif_mdb:citation_author citation_id="3" name="Darke, P.L."> <mmcif_mdb:ordinal>9</mmcif_mdb:ordinal> </mmcif_mdb:citation_author> <mmcif_mdb:citation_author citation_id="4" name="Darke, P.L."> <mmcif_mdb:ordinal>1</mmcif_mdb:ordinal> </mmcif_mdb:citation_author> <mmcif_mdb:citation_author citation_id="4" name="Leu, C.-T."> <mmcif_mdb:ordinal>2</mmcif_mdb:ordinal> </mmcif_mdb:citation_author> <mmcif_mdb:citation_author citation_id="4" name="Davis, L.J."> <mmcif_mdb:ordinal>3</mmcif_mdb:ordinal> </mmcif_mdb:citation_author> <mmcif_mdb:citation_author citation_id="4" name="Heimbach, J.C."> <mmcif_mdb:ordinal>4</mmcif_mdb:ordinal> </mmcif_mdb:citation_author> <mmcif_mdb:citation_author citation_id="4" name="Diehl, R.E."> <mmcif_mdb:ordinal>5</mmcif_mdb:ordinal> </mmcif_mdb:citation_author> <mmcif_mdb:citation_author citation_id="4" name="Hill, W.S."> <mmcif_mdb:ordinal>6</mmcif_mdb:ordinal> </mmcif_mdb:citation_author> <mmcif_mdb:citation_author citation_id="4" name="Dixon, R.A.F."> <mmcif_mdb:ordinal>7</mmcif_mdb:ordinal> </mmcif_mdb:citation_author> <mmcif_mdb:citation_author citation_id="4" name="Sigal, I.S."> <mmcif_mdb:ordinal>8</mmcif_mdb:ordinal> </mmcif_mdb:citation_author> </mmcif_mdb: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 journal articles, books 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 editors associated with the books or book chapters cited in the CITATION list. Example 1 - hypothetical example. <mmcif_mdb:citation_editorCategory> <mmcif_mdb:citation_editor citation_id="5" name="McKeever, B.M."></mmcif_mdb:citation_editor> <mmcif_mdb:citation_editor citation_id="5" name="Navia, M.A."></mmcif_mdb:citation_editor> <mmcif_mdb:citation_editor citation_id="5" name="Fitzgerald, P.M.D."></mmcif_mdb:citation_editor> <mmcif_mdb:citation_editor citation_id="5" name="Springer, J.P."></mmcif_mdb:citation_editor> </mmcif_mdb: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 books 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 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 a more detailed description of computer programs and their attributes to be given, would be used instead. Example 1 - Rodr\'iguez-Romera, Ruiz-P\'erez & Solans [Acta Cryst. (1996), C52, 1415-1417]. Software used for cell refinement. 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 (Hall & Stewart, 1990) Software used for molecular graphics. Give the program or package name and a brief reference. FRODO (Jones, 1986), ORTEP (Johnson, 1965) Software used for generating material for publication. Give the program or package name and a brief reference. Software used for refinement of the structure. Give the program or package name and a brief reference. SHELX85 (Sheldrick, 1985) X-PLOR (Brunger, 1992) 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 CIFs. The ASTM CODEN designator for a journal as given in the Chemical Source List maintained by the Chemical Abstracts Service. The journal code used in the Cambridge Structural Database. This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the DATABASE_2 category record details about the database identifiers of the data block. These data items are assigned by database managers and should only appear in a data block if they originate from that source. The name of this category, DATABASE_2, arose because the category name DATABASE was already in use in the core CIF dictionary, but was used differently from the way it needed to be used in the mmCIF dictionary. Since CIF data names cannot be changed once they have been adopted, a new category had to be created. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <mmcif_mdb:database_2Category> <mmcif_mdb:database_2 database_code="5HVP" database_id="PDB"></mmcif_mdb:database_2> </mmcif_mdb:database_2Category> The code assigned by the database identified in attribute database_id in category database_2. 1ABC ABCDEF An abbreviation that identifies the database. 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 - hypothetical example. <mmcif_mdb:database_PDB_caveatCategory> <mmcif_mdb:database_PDB_caveat id="1"> <mmcif_mdb:text> THE CRYSTAL TRANSFORMATION IS IN ERROR BUT IS</mmcif_mdb:text> </mmcif_mdb:database_PDB_caveat> <mmcif_mdb:database_PDB_caveat id="2"> <mmcif_mdb:text> UNCORRECTABLE AT THIS TIME</mmcif_mdb:text> </mmcif_mdb:database_PDB_caveat> </mmcif_mdb: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 [3][3] 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. <mmcif_mdb:database_PDB_remarkCategory> <mmcif_mdb:database_PDB_remark id="3"> <mmcif_mdb:text> REFINEMENT. BY THE RESTRAINED LEAST-SQUARES PROCEDURE OF J. KONNERT AND W. HENDRICKSON (PROGRAM *PROLSQ*). THE R VALUE IS 0.176 FOR 12901 REFLECTIONS IN THE RESOLUTION RANGE 8.0 TO 2.0 ANGSTROMS WITH I .GT. SIGMA(I). RMS DEVIATIONS FROM IDEAL VALUES (THE VALUES OF SIGMA, IN PARENTHESES, ARE THE INPUT ESTIMATED STANDARD DEVIATIONS THAT DETERMINE THE RELATIVE WEIGHTS OF THE CORRESPONDING RESTRAINTS) DISTANCE RESTRAINTS (ANGSTROMS) BOND DISTANCE 0.018(0.020) ANGLE DISTANCE 0.038(0.030) PLANAR 1-4 DISTANCE 0.043(0.040) PLANE RESTRAINT (ANGSTROMS) 0.015(0.020) CHIRAL-CENTER RESTRAINT (ANGSTROMS**3) 0.177(0.150) NON-BONDED CONTACT RESTRAINTS (ANGSTROMS) SINGLE TORSION CONTACT 0.216(0.500) MULTIPLE TORSION CONTACT 0.207(0.500) POSSIBLE HYDROGEN BOND 0.245(0.500) CONFORMATIONAL TORSION ANGLE RESTRAINT (DEGREES) PLANAR (OMEGA) 2.6(3.0) STAGGERED 17.4(15.0) ORTHONORMAL 18.1(20.0)</mmcif_mdb:text> </mmcif_mdb:database_PDB_remark> <mmcif_mdb:database_PDB_remark id="4"> <mmcif_mdb:text> THE TWO CHAINS OF THE DIMERIC ENZYME HAS BEEN ASSIGNED THE THE CHAIN INDICATORS *A* AND *B*.</mmcif_mdb:text> </mmcif_mdb:database_PDB_remark> </mmcif_mdb: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. <mmcif_mdb:database_PDB_revCategory> <mmcif_mdb:database_PDB_rev num="1"> <mmcif_mdb:author_name>Fitzgerald, Paula M.D</mmcif_mdb:author_name> <mmcif_mdb:date>1991-10-15</mmcif_mdb:date> <mmcif_mdb:date_original>1990-04-30</mmcif_mdb:date_original> <mmcif_mdb:mod_type>0</mmcif_mdb:mod_type> <mmcif_mdb:status>full release</mmcif_mdb:status> </mmcif_mdb:database_PDB_rev> </mmcif_mdb: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 at http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html for details. The PDB code for a subsequent PDB entry that replaced the PDB file corresponding to this data block. The PDB code for a previous PDB entry that was replaced by the PDB file corresponding to this data block. The status of this revision. The value of attribute num in category database_PDB_rev must uniquely and sequentially identify a record in the DATABASE_PDB_REV list. Note that this item must be a number and that modification numbers are assigned in increasing numerical order. Data items in the DATABASE_PDB_REV_RECORD category record details about specific record types that were changed in a given revision of a PDB entry. These data items are assigned by the PDB database managers and should only appear in a data block if they originate from that source. Example 1 - hypothetical example. <mmcif_mdb:database_PDB_rev_recordCategory> <mmcif_mdb:database_PDB_rev_record rev_num="1" type="CONECT"> <mmcif_mdb:details> Error fix - incorrect connection between atoms 2312 and 2317</mmcif_mdb:details> </mmcif_mdb:database_PDB_rev_record> <mmcif_mdb:database_PDB_rev_record rev_num="2" type="MATRIX"> <mmcif_mdb:details>For consistency with 1995-08-04 style-guide</mmcif_mdb:details> </mmcif_mdb:database_PDB_rev_record> <mmcif_mdb:database_PDB_rev_record rev_num="3" type="ORIGX"> <mmcif_mdb:details>Based on new data from author</mmcif_mdb:details> </mmcif_mdb:database_PDB_rev_record> </mmcif_mdb: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 the 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 their measurement. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <mmcif_mdb:diffrnCategory> <mmcif_mdb:diffrn id="Set1"> <mmcif_mdb:ambient_environment> Mother liquor from the reservoir of the vapor diffusion experiment, mounted in room air</mmcif_mdb:ambient_environment> <mmcif_mdb:ambient_temp>293(3)</mmcif_mdb:ambient_temp> <mmcif_mdb:crystal_support> 0.7 mm glass capillary, sealed with dental wax</mmcif_mdb:crystal_support> <mmcif_mdb:crystal_treatment> Equilibrated in rotating anode radiation enclosure for 18 hours prior to beginning of data collection</mmcif_mdb:crystal_treatment> </mmcif_mdb:diffrn> </mmcif_mdb:diffrnCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. <mmcif_mdb:diffrnCategory> <mmcif_mdb:diffrn id="d1"> <mmcif_mdb:ambient_temp>293</mmcif_mdb:ambient_temp> <mmcif_mdb: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.</mmcif_mdb:details> </mmcif_mdb:diffrn> </mmcif_mdb:diffrnCategory> The gas or liquid surrounding the sample, if not air. The mean temperature in kelvins at which the intensities were measured. A description of special aspects of temperature control during data collection. The standard uncertainty (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 [Acta Cryst. (1991), C47, 2276-2277]. <mmcif_mdb:diffrn_attenuatorCategory> <mmcif_mdb:diffrn_attenuator code="1"> <mmcif_mdb:scale>16.976</mmcif_mdb:scale> </mmcif_mdb:diffrn_attenuator> </mmcif_mdb:diffrn_attenuatorCategory> The scale factor applied when an intensity measurement is reduced by an attenuator identified by attribute code. in category diffrn_attenuator The measured intensity must be multiplied by this scale 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. <mmcif_mdb:diffrn_detectorCategory> <mmcif_mdb:diffrn_detector diffrn_id="d1"> <mmcif_mdb:detector>multiwire</mmcif_mdb:detector> <mmcif_mdb:type>Siemens</mmcif_mdb:type> </mmcif_mdb:diffrn_detector> </mmcif_mdb:diffrn_detectorCategory> A description of special aspects of the radiation detector. The general class of the radiation detector. photographic film scintillation counter CCD plate BF~3~ counter 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. <mmcif_mdb:diffrn_measurementCategory> <mmcif_mdb:diffrn_measurement diffrn_id="d1"> <mmcif_mdb:details> 440 frames, 0.20 degrees, 150 sec, detector distance 12 cm, detector angle 22.5 degrees</mmcif_mdb:details> <mmcif_mdb:device>3-circle camera</mmcif_mdb:device> <mmcif_mdb:device_details>none</mmcif_mdb:device_details> <mmcif_mdb:device_type>Supper model x</mmcif_mdb:device_type> <mmcif_mdb:method>omega scan</mmcif_mdb:method> </mmcif_mdb:diffrn_measurement> </mmcif_mdb:diffrn_measurementCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <mmcif_mdb:diffrn_measurementCategory> <mmcif_mdb:diffrn_measurement diffrn_id="s1"> <mmcif_mdb:device_type>Philips PW1100/20 diffractometer</mmcif_mdb:device_type> <mmcif_mdb:method>\q/2\q</mmcif_mdb:method> </mmcif_mdb:diffrn_measurement> </mmcif_mdb: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. commercial goniometer modified locally to allow for 90\% \t arc The make, model or name of the measurement device (goniometer) used. Supper model q Huber model r Enraf-Nonius model s homemade Method used to measure intensities. profile data from theta/2theta scans The physical device used to support the crystal during data collection. glass capillary quartz capillary fiber metal loop This data item is a pointer to attribute id in category diffrn in the DIFFRN category. Data items in the DIFFRN_ORIENT_MATRIX category record details about the orientation matrix used in the measurement of the diffraction data. Example 1 - based on CAD-4 diffractometer data obtained for Yb(S-C5H4N)2(THF)4. <mmcif_mdb:diffrn_orient_matrixCategory> <mmcif_mdb:diffrn_orient_matrix diffrn_id="set1"> <mmcif_mdb:UB11>-0.071479</mmcif_mdb:UB11> <mmcif_mdb:UB12>0.020208</mmcif_mdb:UB12> <mmcif_mdb:UB13>0.039076</mmcif_mdb:UB13> <mmcif_mdb:UB21>0.035372</mmcif_mdb:UB21> <mmcif_mdb:UB22>0.056209</mmcif_mdb:UB22> <mmcif_mdb:UB23>0.078324</mmcif_mdb:UB23> <mmcif_mdb:UB31>-0.007470</mmcif_mdb:UB31> <mmcif_mdb:UB32>0.067854</mmcif_mdb:UB32> <mmcif_mdb:UB33>-0.017832</mmcif_mdb:UB33> <mmcif_mdb:type> reciprocal axis matrix, multiplies hkl vector to generate diffractometer xyz vector and diffractometer angles</mmcif_mdb:type> </mmcif_mdb:diffrn_orient_matrix> </mmcif_mdb:diffrn_orient_matrixCategory> The [1][1] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect 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 with respect 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 with respect 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 with respect 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 with respect 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 with respect 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 with respect 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 with respect 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 with respect 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 the measurement of the diffraction intensities. Example 1 - based on CAD-4 diffractometer data obtained for Yb(S-C5H4N)2(THF)4. <mmcif_mdb:diffrn_orient_reflnCategory> <mmcif_mdb:diffrn_orient_refln diffrn_id="myset1" index_h="2" index_k="0" index_l="2"> <mmcif_mdb:angle_chi>-28.45</mmcif_mdb:angle_chi> <mmcif_mdb:angle_kappa>-11.32</mmcif_mdb:angle_kappa> <mmcif_mdb:angle_omega>5.33</mmcif_mdb:angle_omega> <mmcif_mdb:angle_phi>101.78</mmcif_mdb:angle_phi> <mmcif_mdb:angle_psi>0.00</mmcif_mdb:angle_psi> <mmcif_mdb:angle_theta>10.66</mmcif_mdb:angle_theta> </mmcif_mdb:diffrn_orient_refln> </mmcif_mdb:diffrn_orient_reflnCategory> Diffractometer angle chi of a reflection used to define the orientation matrix in degrees. See attribute UB[][] in category diffrn_orient_matrix and the Miller indices in the DIFFRN_ORIENT_REFLN category. Diffractometer angle kappa of a reflection used to define the orientation matrix in degrees. See attribute UB[][] in category diffrn_orient_matrix and the Miller indices in the DIFFRN_ORIENT_REFLN category. Diffractometer angle omega of a reflection used to define the orientation matrix in degrees. See attribute UB[][] in category diffrn_orient_matrix and the Miller indices in the DIFFRN_ORIENT_REFLN category. Diffractometer angle phi of a reflection used to define the orientation matrix in degrees. See attribute UB[][] in category diffrn_orient_matrix and the Miller indices in the DIFFRN_ORIENT_REFLN category. Diffractometer angle psi of a reflection used to define the orientation matrix in degrees. See attribute UB[][] in category diffrn_orient_matrix and the Miller indices in the DIFFRN_ORIENT_REFLN category. Diffractometer angle theta of a reflection used to define the orientation matrix in degrees. 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 the diffraction intensities, its collimation and monochromatization 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. <mmcif_mdb:diffrn_radiationCategory> <mmcif_mdb:diffrn_radiation diffrn_id="set1"> <mmcif_mdb:collimation>0.3 mm double pinhole</mmcif_mdb:collimation> <mmcif_mdb:monochromator>graphite</mmcif_mdb:monochromator> <mmcif_mdb:type>Cu K\a</mmcif_mdb:type> <mmcif_mdb:wavelength_id>1</mmcif_mdb:wavelength_id> </mmcif_mdb:diffrn_radiation> </mmcif_mdb:diffrn_radiationCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. 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 The angle in degrees, as viewed from the specimen, between the perpendicular component of the polarization and the diffraction plane. See attribute polarisn_ratio in category diffrn_radiation. Polarization ratio of the diffraction beam incident on the crystal. This is the ratio of the perpendicularly polarized to the parallel-polarized 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). The nature of the radiation used (i.e. the name of the subatomic particle or the region of the electromagnetic spectrum). It is strongly recommended that this information is given, so that the probe radiation can be simply determined. The nature of the radiation. This is typically a description of the X-ray wavelength in Siegbahn notation. CuK\a Cu K\a~1~ Cu K-L~2,3~ white-beam This data item is a pointer to attribute id in category diffrn_radiation_wavelength in the DIFFRN_RADIATION_WAVELENGTH category. The IUPAC symbol for the X-ray wavelength for the 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 the radiation used to measure the 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. <mmcif_mdb:diffrn_radiation_wavelengthCategory> <mmcif_mdb:diffrn_radiation_wavelength id="1"> <mmcif_mdb:wavelength>1.54</mmcif_mdb:wavelength> <mmcif_mdb:wt>1.0</mmcif_mdb:wt> </mmcif_mdb:diffrn_radiation_wavelength> </mmcif_mdb: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 wavelength. 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 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. <mmcif_mdb:diffrn_reflnCategory> <mmcif_mdb:diffrn_refln diffrn_id="set1" id="1102"> <mmcif_mdb:angle_chi>32.21</mmcif_mdb:angle_chi> <mmcif_mdb:angle_kappa>20.12</mmcif_mdb:angle_kappa> <mmcif_mdb:angle_omega>11.54</mmcif_mdb:angle_omega> <mmcif_mdb:angle_phi>176.02</mmcif_mdb:angle_phi> <mmcif_mdb:angle_psi>0.00</mmcif_mdb:angle_psi> <mmcif_mdb:angle_theta>23.08</mmcif_mdb:angle_theta> <mmcif_mdb:attenuator_code>Ni.005</mmcif_mdb:attenuator_code> <mmcif_mdb:counts_bg_1>22</mmcif_mdb:counts_bg_1> <mmcif_mdb:counts_bg_2>25</mmcif_mdb:counts_bg_2> <mmcif_mdb:counts_net>3450</mmcif_mdb:counts_net> <mmcif_mdb:counts_peak>321</mmcif_mdb:counts_peak> <mmcif_mdb:counts_total>3499</mmcif_mdb:counts_total> <mmcif_mdb:detect_slit_horiz>0.04</mmcif_mdb:detect_slit_horiz> <mmcif_mdb:detect_slit_vert>0.02</mmcif_mdb:detect_slit_vert> <mmcif_mdb:elapsed_time>1.00</mmcif_mdb:elapsed_time> <mmcif_mdb:index_h>4</mmcif_mdb:index_h> <mmcif_mdb:index_k>0</mmcif_mdb:index_k> <mmcif_mdb:index_l>2</mmcif_mdb:index_l> <mmcif_mdb:intensity_net>202.56</mmcif_mdb:intensity_net> <mmcif_mdb:intensity_sigma>2.18</mmcif_mdb:intensity_sigma> <mmcif_mdb:scale_group_code>A24</mmcif_mdb:scale_group_code> <mmcif_mdb:scan_mode>om</mmcif_mdb:scan_mode> <mmcif_mdb:scan_mode_backgd>mo</mmcif_mdb:scan_mode_backgd> <mmcif_mdb:scan_rate>1.2</mmcif_mdb:scan_rate> <mmcif_mdb:scan_time_backgd>900.00</mmcif_mdb:scan_time_backgd> <mmcif_mdb:scan_width>1.0</mmcif_mdb:scan_width> <mmcif_mdb:sint_over_lambda>0.25426</mmcif_mdb:sint_over_lambda> <mmcif_mdb:standard_code>1</mmcif_mdb:standard_code> <mmcif_mdb:wavelength>1.54184</mmcif_mdb:wavelength> <mmcif_mdb:wavelength_id>Cu1fixed</mmcif_mdb:wavelength_id> </mmcif_mdb:diffrn_refln> </mmcif_mdb:diffrn_reflnCategory> The diffractometer angle chi of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. The diffractometer angle kappa of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. The diffractometer angle omega of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. The diffractometer angle phi of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. The diffractometer angle psi of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. The diffractometer angle theta of a reflection in degrees. 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 the diffraction experiment to the measurement of this intensity. Miller index h of a 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 given in attribute reduction_process in category diffrn_reflns. See also attribute transf_matrix[][] in category diffrn_reflns. Miller index k of a 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 given in attribute reduction_process in category diffrn_reflns. See also attribute transf_matrix[][] in category diffrn_reflns. Miller index l of a 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 given 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 (estimated standard deviation) 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 for measurements using 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 in degrees per minute to measure the intensity. 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 the 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 attribute id in category diffrn_refln 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 absolute 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 Miller index h for the reflection data specified by attribute index_h in category diffrn_refln. The minimum value of the Miller index h for the reflection data specified by attribute index_h in category diffrn_refln. The maximum value of the Miller index k for the reflection data specified by attribute index_k in category diffrn_refln. The minimum value of the Miller index k for the reflection data specified by attribute index_k in category diffrn_refln. The maximum value of the Miller index l for the reflection data specified by attribute index_l in category diffrn_refln. The minimum value of the Miller index l for the 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 of the scaling factors applied to place all intensities in the reflection lists on a common scale. Scaling groups might, for example, 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. <mmcif_mdb:diffrn_scale_groupCategory> <mmcif_mdb:diffrn_scale_group code="A24"> <mmcif_mdb:I_net>1.021</mmcif_mdb:I_net> </mmcif_mdb:diffrn_scale_group> </mmcif_mdb: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 attribute code in category diffrn_scale_group 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. <mmcif_mdb:diffrn_sourceCategory> <mmcif_mdb:diffrn_source diffrn_id="s1"> <mmcif_mdb:current>180</mmcif_mdb:current> <mmcif_mdb:power>50</mmcif_mdb:power> <mmcif_mdb:size>8mm x 0.4 mm broad-focus</mmcif_mdb:size> <mmcif_mdb:source>rotating anode</mmcif_mdb:source> <mmcif_mdb:type>Rigaku RU-200</mmcif_mdb:type> </mmcif_mdb:diffrn_source> </mmcif_mdb:diffrn_sourceCategory> The current in milliamperes at which the radiation source was operated. A description of special aspects of the radiation source used. 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 to generate X-rays. This can also be used 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 [Acta Cryst. (1991), C47, 2276-2277]. <mmcif_mdb:diffrn_standard_reflnCategory> <mmcif_mdb:diffrn_standard_refln code="1" diffrn_id="s1"> <mmcif_mdb:index_h>3</mmcif_mdb:index_h> <mmcif_mdb:index_k>2</mmcif_mdb:index_k> <mmcif_mdb:index_l>4</mmcif_mdb:index_l> </mmcif_mdb:diffrn_standard_refln> <mmcif_mdb:diffrn_standard_refln code="1" diffrn_id="s1"> <mmcif_mdb:index_h>1</mmcif_mdb:index_h> <mmcif_mdb:index_k>9</mmcif_mdb:index_k> <mmcif_mdb:index_l>1</mmcif_mdb:index_l> </mmcif_mdb:diffrn_standard_refln> <mmcif_mdb:diffrn_standard_refln code="1" diffrn_id="s1"> <mmcif_mdb:index_h>3</mmcif_mdb:index_h> <mmcif_mdb:index_k>0</mmcif_mdb:index_k> <mmcif_mdb:index_l>10</mmcif_mdb:index_l> </mmcif_mdb:diffrn_standard_refln> </mmcif_mdb: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. 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 This data item is a pointer to attribute id in category diffrn in the DIFFRN category. Data items in the DIFFRN_STANDARDS category record details about the set of standard reflections used to monitor intensity stability during the measurement of diffraction intensities. Note that these records describe properties common to the set of standard reflections, not the standard reflections themselves. Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <mmcif_mdb:diffrn_standardsCategory> <mmcif_mdb:diffrn_standards diffrn_id="s1"> <mmcif_mdb:decay_>0</mmcif_mdb:decay_> <mmcif_mdb:interval_time>120</mmcif_mdb:interval_time> <mmcif_mdb:number>3</mmcif_mdb:number> </mmcif_mdb:diffrn_standards> </mmcif_mdb:diffrn_standardsCategory> The percentage decrease in the mean of the intensities for the set of standard reflections from the start of the measurement process to the end. 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 during the measurement of the diffraction intensities. The standard uncertainty (estimated standard deviation) 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 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 subcategories 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 by 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. <mmcif_mdb:entityCategory> <mmcif_mdb:entity id="1"> <mmcif_mdb:details> The enzymatically competent form of HIV protease is a dimer. This entity corresponds to one monomer of an active dimer.</mmcif_mdb:details> <mmcif_mdb:formula_weight>10916</mmcif_mdb:formula_weight> <mmcif_mdb:type>polymer</mmcif_mdb:type> </mmcif_mdb:entity> <mmcif_mdb:entity id="2"> <mmcif_mdb:details></mmcif_mdb:details> <mmcif_mdb:formula_weight>762</mmcif_mdb:formula_weight> <mmcif_mdb:type>non-polymer</mmcif_mdb:type> </mmcif_mdb:entity> <mmcif_mdb:entity id="3"> <mmcif_mdb:details></mmcif_mdb:details> <mmcif_mdb:formula_weight>18</mmcif_mdb:formula_weight> <mmcif_mdb:type>water</mmcif_mdb:type> </mmcif_mdb:entity> </mmcif_mdb:entityCategory> A description of special aspects of the entity. Formula mass in daltons of the entity. 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, not cytokines or beta-alpha-barrels, and polyribonucleic acids are simply poly-RNA, not transfer- RNA. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <mmcif_mdb:entity_keywordsCategory> <mmcif_mdb:entity_keywords entity_id="1" text="polypeptide"></mmcif_mdb:entity_keywords> <mmcif_mdb:entity_keywords entity_id="2" text="natural product, inhibitor, reduced peptide"></mmcif_mdb:entity_keywords> </mmcif_mdb:entity_keywordsCategory> This data item is a pointer to attribute id in category entity in the ENTITY category. Keywords describing this entity. polypeptide natural product polysaccharide Data items in the ENTITY_LINK category give details about the links between entities. A description of special aspects of a link between chemical components in the structure. The entity ID of the first of the two entities joined by the link. 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 link. 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 link. 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 link. 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 example, haemoglobin alpha chain would be the entity common name, not haemoglobin. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <mmcif_mdb:entity_name_comCategory> <mmcif_mdb:entity_name_com entity_id="1" name="HIV-1 protease monomer"></mmcif_mdb:entity_name_com> <mmcif_mdb:entity_name_com entity_id="1" name="HIV-1 PR monomer"></mmcif_mdb:entity_name_com> <mmcif_mdb:entity_name_com entity_id="2" name="acetyl-pepstatin"></mmcif_mdb:entity_name_com> <mmcif_mdb:entity_name_com entity_id="2" name="acetyl-Ile-Val-Asp-Statine-Ala-Ile-Statine"></mmcif_mdb:entity_name_com> <mmcif_mdb:entity_name_com entity_id="3" name="water"></mmcif_mdb:entity_name_com> </mmcif_mdb: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 arbutin Data items in the ENTITY_NAME_SYS category record the systematic name or names associated with the entity and the system that was used to construct the systematic name. In some cases, the entity name may not be the same as the name of the biological structure. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <mmcif_mdb:entity_name_sysCategory> <mmcif_mdb:entity_name_sys entity_id="1" name="EC 3.4.23.16"></mmcif_mdb:entity_name_sys> <mmcif_mdb:entity_name_sys entity_id="2" name="acetyl-Ile-Val-Asp-Sta-Ala-Ile-Sta"></mmcif_mdb:entity_name_sys> <mmcif_mdb:entity_name_sys entity_id="3" name="water"></mmcif_mdb:entity_name_sys> </mmcif_mdb: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. hydroquinone-beta-D-pyranoside EC 2.1.1.1 2-fluoro-1,4-dichlorobenzene 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 nonstandard features. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <mmcif_mdb:entity_polyCategory> <mmcif_mdb:entity_poly entity_id="1"> <mmcif_mdb:nstd_chirality>no</mmcif_mdb:nstd_chirality> <mmcif_mdb:nstd_linkage>no</mmcif_mdb:nstd_linkage> <mmcif_mdb:nstd_monomer>no</mmcif_mdb:nstd_monomer> <mmcif_mdb:type>polypeptide(L)</mmcif_mdb:type> <mmcif_mdb:type_details></mmcif_mdb:type_details> </mmcif_mdb:entity_poly> </mmcif_mdb:entity_polyCategory> A flag to indicate whether 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 the polymer contains at least one monomer-to-monomer link different from that implied by attribute type in category entity_poly. A flag to indicate whether the polymer contains at least one monomer that is not considered standard. The number of monomers in the polymer. 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. <mmcif_mdb:entity_poly_seqCategory> <mmcif_mdb:entity_poly_seq entity_id="1" mon_id="PRO" num="1"></mmcif_mdb:entity_poly_seq> <mmcif_mdb:entity_poly_seq entity_id="1" mon_id="GLN" num="2"></mmcif_mdb:entity_poly_seq> <mmcif_mdb:entity_poly_seq entity_id="1" mon_id="ILE" num="3"></mmcif_mdb:entity_poly_seq> <mmcif_mdb:entity_poly_seq entity_id="1" mon_id="THR" num="4"></mmcif_mdb:entity_poly_seq> <mmcif_mdb:entity_poly_seq entity_id="1" mon_id="LEU" num="5"></mmcif_mdb:entity_poly_seq> <mmcif_mdb:entity_poly_seq entity_id="1" mon_id="TRP" num="6"></mmcif_mdb:entity_poly_seq> <mmcif_mdb:entity_poly_seq entity_id="1" mon_id="GLN" num="7"></mmcif_mdb:entity_poly_seq> <mmcif_mdb:entity_poly_seq entity_id="1" mon_id="ARG" num="8"></mmcif_mdb:entity_poly_seq> <mmcif_mdb:entity_poly_seq entity_id="1" mon_id="PRO" num="9"></mmcif_mdb:entity_poly_seq> <mmcif_mdb:entity_poly_seq entity_id="1" mon_id="LEU" num="10"></mmcif_mdb:entity_poly_seq> <mmcif_mdb:entity_poly_seq entity_id="1" mon_id="VAL" num="11"></mmcif_mdb:entity_poly_seq> <mmcif_mdb:entity_poly_seq entity_id="1" mon_id="THR" num="12"></mmcif_mdb:entity_poly_seq> <mmcif_mdb:entity_poly_seq entity_id="1" mon_id="ILE" num="13"></mmcif_mdb:entity_poly_seq> <mmcif_mdb:entity_poly_seq entity_id="1" mon_id="LYS" num="14"></mmcif_mdb:entity_poly_seq> <mmcif_mdb:entity_poly_seq entity_id="1" mon_id="ILE" num="15"></mmcif_mdb:entity_poly_seq> <mmcif_mdb:entity_poly_seq entity_id="1" mon_id="GLY" num="16"></mmcif_mdb:entity_poly_seq> <mmcif_mdb:entity_poly_seq entity_id="1" mon_id="GLY" num="17"></mmcif_mdb:entity_poly_seq> <mmcif_mdb:entity_poly_seq entity_id="1" mon_id="GLN" num="18"></mmcif_mdb:entity_poly_seq> <mmcif_mdb:entity_poly_seq entity_id="1" mon_id="LEU" num="19"></mmcif_mdb:entity_poly_seq> <mmcif_mdb:entity_poly_seq entity_id="1" mon_id="LYS" num="20"></mmcif_mdb:entity_poly_seq> <mmcif_mdb:entity_poly_seq entity_id="1" mon_id="GLU" num="21"></mmcif_mdb:entity_poly_seq> <mmcif_mdb:entity_poly_seq entity_id="1" mon_id="ALA" num="22"></mmcif_mdb:entity_poly_seq> <mmcif_mdb:entity_poly_seq entity_id="1" mon_id="LEU" num="23"></mmcif_mdb:entity_poly_seq> <mmcif_mdb:entity_poly_seq entity_id="1" mon_id="LEU" num="24"></mmcif_mdb:entity_poly_seq> <mmcif_mdb:entity_poly_seq entity_id="1" mon_id="ASP" num="25"></mmcif_mdb:entity_poly_seq> </mmcif_mdb:entity_poly_seqCategory> A flag to indicate whether this monomer in the polymer is heterogeneous in sequence. This would be rare. This data item is a pointer to attribute id in category entity in the ENTITY category. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP 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. Data items in the ENTITY_SRC_GEN category record details of the source from which the entity was obtained in cases where the source was genetically manipulated. 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. <mmcif_mdb:entity_src_genCategory> <mmcif_mdb:entity_src_gen entity_id="1"> <mmcif_mdb:gene_src_common_name>HIV-1</mmcif_mdb:gene_src_common_name> <mmcif_mdb:gene_src_genus xsi:nil="true" /> <mmcif_mdb:gene_src_species xsi:nil="true" /> <mmcif_mdb:gene_src_strain>NY-5</mmcif_mdb:gene_src_strain> <mmcif_mdb:host_org_common_name>bacteria</mmcif_mdb:host_org_common_name> <mmcif_mdb:host_org_genus>Escherichia</mmcif_mdb:host_org_genus> <mmcif_mdb:host_org_species>coli</mmcif_mdb:host_org_species> <mmcif_mdb:plasmid_name>pB322</mmcif_mdb:plasmid_name> </mmcif_mdb:entity_src_gen> </mmcif_mdb: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 subcellular 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 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 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. <mmcif_mdb:entity_src_natCategory> <mmcif_mdb:entity_src_nat entity_id="2"> <mmcif_mdb:common_name>bacteria</mmcif_mdb:common_name> <mmcif_mdb: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.</mmcif_mdb:details> <mmcif_mdb:genus>Actinomycetes</mmcif_mdb:genus> <mmcif_mdb:species xsi:nil="true" /> </mmcif_mdb:entity_src_nat> </mmcif_mdb:entity_src_natCategory> The common name 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 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 subcellular 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. <mmcif_mdb:entryCategory> <mmcif_mdb:entry id="5HVP"></mmcif_mdb:entry> </mmcif_mdb:entryCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <mmcif_mdb:entryCategory> <mmcif_mdb:entry id="TOZ"></mmcif_mdb:entry> </mmcif_mdb: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~. <mmcif_mdb:entry_linkCategory> <mmcif_mdb:entry_link entry_id="KSE_TEXT" id="KSE_COM"> <mmcif_mdb:details>experimental data common to ref./mod. structures</mmcif_mdb:details> </mmcif_mdb:entry_link> <mmcif_mdb:entry_link entry_id="KSE_TEXT" id="KSE_REF"> <mmcif_mdb:details>reference structure</mmcif_mdb:details> </mmcif_mdb:entry_link> <mmcif_mdb:entry_link entry_id="KSE_TEXT" id="KSE_MOD"> <mmcif_mdb:details>modulated structure</mmcif_mdb:details> </mmcif_mdb:entry_link> </mmcif_mdb:entry_linkCategory> A description of the relationship between the data blocks identified by _entry_link.id and _entry_link.entry_id. This data item is a pointer to attribute id in category entry in the ENTRY category. The value of attribute id in category entry_link identifies a data block related to the current data block. Data items in the EXPTL category record details about the experimental work prior to the intensity measurements and details about the absorption-correction technique employed. Example 1 - based on laboratory records for Yb(S-C5H4N)2(THF)4. <mmcif_mdb:exptlCategory> <mmcif_mdb:exptl entry_id="datablock1"> <mmcif_mdb:absorpt_coefficient_mu>1.22</mmcif_mdb:absorpt_coefficient_mu> <mmcif_mdb:absorpt_correction_T_max>0.896</mmcif_mdb:absorpt_correction_T_max> <mmcif_mdb:absorpt_correction_T_min>0.802</mmcif_mdb:absorpt_correction_T_min> <mmcif_mdb:absorpt_correction_type>integration</mmcif_mdb:absorpt_correction_type> <mmcif_mdb:absorpt_process_details> Gaussian grid method from SHELX76 Sheldrick, G. M., &quot;SHELX-76: structure determination and refinement program&quot;, Cambridge University, UK, 1976</mmcif_mdb:absorpt_process_details> <mmcif_mdb:crystals_number>1</mmcif_mdb:crystals_number> <mmcif_mdb:details> Enraf-Nonius LT2 liquid nitrogen variable-temperature device used</mmcif_mdb:details> <mmcif_mdb:method>single-crystal x-ray diffraction</mmcif_mdb:method> <mmcif_mdb:method_details> graphite monochromatized Cu K(alpha) fixed tube and Enraf-Nonius CAD4 diffractometer used</mmcif_mdb:method_details> </mmcif_mdb:exptl> </mmcif_mdb: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 factor for the crystal and radiation. The maximum and minimum transmission factors are also referred to as the absorption correction A or 1/A*. The minimum transmission factor for the crystal and radiation. The maximum and minimum transmission 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 more detailed information is not 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 nmr 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 the results of experimental measurements on the crystal or crystals used, such as shape, size or density. Example 1 - based on laboratory records for Yb(S-C5H4N)2(THF)4. <mmcif_mdb:exptl_crystalCategory> <mmcif_mdb:exptl_crystal id="xst2l"> <mmcif_mdb:F_000>202</mmcif_mdb:F_000> <mmcif_mdb:colour>pale yellow</mmcif_mdb:colour> <mmcif_mdb:density_Matthews>1.01</mmcif_mdb:density_Matthews> <mmcif_mdb:density_diffrn>1.113</mmcif_mdb:density_diffrn> <mmcif_mdb:density_method>neutral buoyancy</mmcif_mdb:density_method> <mmcif_mdb:density_percent_sol>0.15</mmcif_mdb:density_percent_sol> <mmcif_mdb:description>hexagonal rod, uncut</mmcif_mdb:description> <mmcif_mdb:preparation> hanging drop, crystal soaked in 10&#37; ethylene glycol for 10 h, then placed in nylon loop at data collection time</mmcif_mdb:preparation> <mmcif_mdb:size_max>0.30</mmcif_mdb:size_max> <mmcif_mdb:size_mid>0.20</mmcif_mdb:size_mid> <mmcif_mdb:size_min>0.05</mmcif_mdb:size_min> <mmcif_mdb:size_rad>0.025</mmcif_mdb:size_rad> </mmcif_mdb:exptl_crystal> </mmcif_mdb:exptl_crystalCategory> Example 2 - using separate items to define upper and lower limits for a value. Example 3 - here the density was measured at some unspecified temperature below room temperature. The effective number of electrons in the crystal unit cell contributing to F(000). This 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 degree f~i~ = imaginary part of the scattering factors at theta = 0 degree the sum is taken over each atom in the unit cell 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. (1968). J. Mol. Biol. 33, 491-497. Density values calculated from the crystal cell and contents. The units are megagrams per cubic metre (grams per cubic centimetre). The method used to measure attribute density_meas in category exptl_crystal. Density value P calculated from the crystal cell and contents, expressed as per cent 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 = a conversion factor evaluated as: (0.74 cm^3^/g) (10^24^ A^3^/cm^3^) -------------------------------------- (6.02*10^23^) molecules/mole 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. The crystal dimensions should not normally be reported here; use instead the specific items in the EXPTL_CRYSTAL category relating to size for the gross dimensions of the crystal and data items in the EXPTL_CRYSTAL_FACE category to describe the relationship between individual faces. 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. <mmcif_mdb:exptl_crystal_faceCategory> <mmcif_mdb:exptl_crystal_face crystal_id="xstl1" index_h="1" index_k="0" index_l="0"> <mmcif_mdb:diffr_chi>42.56</mmcif_mdb:diffr_chi> <mmcif_mdb:diffr_kappa>30.23</mmcif_mdb:diffr_kappa> <mmcif_mdb:diffr_phi>-125.56</mmcif_mdb:diffr_phi> <mmcif_mdb:diffr_psi>-0.34</mmcif_mdb:diffr_psi> <mmcif_mdb:perp_dist>0.025</mmcif_mdb:perp_dist> </mmcif_mdb:exptl_crystal_face> </mmcif_mdb: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 from 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. <mmcif_mdb:exptl_crystal_growCategory> <mmcif_mdb:exptl_crystal_grow crystal_id="1"> <mmcif_mdb:apparatus>Linbro plates</mmcif_mdb:apparatus> <mmcif_mdb:atmosphere>room air</mmcif_mdb:atmosphere> <mmcif_mdb:method>hanging drop</mmcif_mdb:method> <mmcif_mdb:pH>4.7</mmcif_mdb:pH> <mmcif_mdb:temp>18(3)</mmcif_mdb:temp> <mmcif_mdb:time>approximately 2 days</mmcif_mdb:time> </mmcif_mdb:exptl_crystal_grow> </mmcif_mdb: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 standard uncertainty (estimated standard deviation) of attribute pressure in category exptl_crystal_grow. A description of the protocol used for seeding the crystal growth. macroseeding Microcrystals were introduced from a previous crystal growth experiment by transfer with a human hair. A literature reference that describes the protocol used to seed the crystal. Stura et al., 1989 The temperature in kelvins at which the crystal was grown. If more than one temperature was employed during the crystallization process, the final temperature should be noted here and the protocol involving multiple temperatures should be described in attribute details in category exptl_crystal_grow. A description of special aspects of temperature control during crystal growth. The standard uncertainty (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 given in attribute details in category exptl_crystal_grow_comp 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. <mmcif_mdb:exptl_crystal_grow_compCategory> <mmcif_mdb:exptl_crystal_grow_comp crystal_id="1" id="1"> <mmcif_mdb:conc>6 mg/ml</mmcif_mdb:conc> <mmcif_mdb:details> The protein solution was in a buffer containing 25 mM NaCl, 100 mM NaMES/ MES buffer, pH 7.5, 3 mM NaAzide</mmcif_mdb:details> <mmcif_mdb:name>HIV-1 protease</mmcif_mdb:name> <mmcif_mdb:sol_id>1</mmcif_mdb:sol_id> <mmcif_mdb:volume>0.002 ml</mmcif_mdb:volume> </mmcif_mdb:exptl_crystal_grow_comp> <mmcif_mdb:exptl_crystal_grow_comp crystal_id="1" id="2"> <mmcif_mdb:conc>4 M</mmcif_mdb:conc> <mmcif_mdb:details>in 3 mM NaAzide</mmcif_mdb:details> <mmcif_mdb:name>NaCl</mmcif_mdb:name> <mmcif_mdb:sol_id>2</mmcif_mdb:sol_id> <mmcif_mdb:volume>0.200 ml</mmcif_mdb:volume> </mmcif_mdb:exptl_crystal_grow_comp> <mmcif_mdb:exptl_crystal_grow_comp crystal_id="1" id="3"> <mmcif_mdb:conc>100 mM</mmcif_mdb:conc> <mmcif_mdb:details>in 3 mM NaAzide</mmcif_mdb:details> <mmcif_mdb:name>Acetic Acid</mmcif_mdb:name> <mmcif_mdb:sol_id>2</mmcif_mdb:sol_id> <mmcif_mdb:volume>0.047 ml</mmcif_mdb:volume> </mmcif_mdb:exptl_crystal_grow_comp> <mmcif_mdb:exptl_crystal_grow_comp crystal_id="1" id="4"> <mmcif_mdb:conc>100 mM</mmcif_mdb:conc> <mmcif_mdb: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.</mmcif_mdb:details> <mmcif_mdb:name>Na Acetate</mmcif_mdb:name> <mmcif_mdb:sol_id>2</mmcif_mdb:sol_id> <mmcif_mdb:volume>0.053 ml</mmcif_mdb:volume> </mmcif_mdb:exptl_crystal_grow_comp> <mmcif_mdb:exptl_crystal_grow_comp crystal_id="1" id="5"> <mmcif_mdb:conc>neat</mmcif_mdb:conc> <mmcif_mdb:details>in 3 mM NaAzide</mmcif_mdb:details> <mmcif_mdb:name>water</mmcif_mdb:name> <mmcif_mdb:sol_id>2</mmcif_mdb:sol_id> <mmcif_mdb:volume>0.700 ml</mmcif_mdb:volume> </mmcif_mdb:exptl_crystal_grow_comp> </mmcif_mdb:exptl_crystal_grow_compCategory> The concentration of the solution component. 200 \ml 0.1 ml A description of any special aspects of the solution component. When the solution component is the one that contains the macromolecule, this could be the specification of the buffer in which the macromolecule was stored. When the solution component is a buffer component, this could be the methods (or formula) used to achieve a desired pH. in 3 mM NaAzide The protein solution was in a buffer containing 25 mM NaCl, 100 mM NaMES/MES buffer, pH 7.5, 3 mM NaAzide in 3 mM NaAzide. Buffer components were mixed to produce a pH of 4.7 according to a ratio calculated from the pKa. The actual pH of solution 2 was not measured. A common name for the component of the solution. protein in buffer acetic acid An identifier for the solution to which the given solution component belongs. 1 well solution solution A The volume of the solution component. 200 \ml 0.1 ml This data item is a pointer to attribute id in category exptl_crystal in the EXPTL_CRYSTAL category. 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 Data items in the GEOM and related (GEOM_ANGLE, GEOM_BOND, GEOM_CONTACT, GEOM_HBOND and GEOM_TORSION) categories record details about the molecular geometry as calculated from the contents of the ATOM, CELL and SYMMETRY data. Geometry data are therefore redundant, in that they can be calculated from other more fundamental quantities in the data block. However, they provide a check on the correctness of both sets of data and enable the most important geometric data to be identified for publication by setting the appropriate publication flag. A description of geometry not covered by the existing data names in the GEOM categories, such as least-squares planes. This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the GEOM_ANGLE category record details about the bond angles as calculated from the contents of the ATOM, CELL and SYMMETRY data. Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <mmcif_mdb:geom_angleCategory> <mmcif_mdb:geom_angle atom_site_id_1="C2" atom_site_id_2="O1" atom_site_id_3="C5" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <mmcif_mdb:publ_flag>yes</mmcif_mdb:publ_flag> <mmcif_mdb:value>111.6</mmcif_mdb:value> <mmcif_mdb:value_esd>0.2</mmcif_mdb:value_esd> </mmcif_mdb:geom_angle> <mmcif_mdb:geom_angle atom_site_id_1="O1" atom_site_id_2="C2" atom_site_id_3="C3" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <mmcif_mdb:publ_flag>yes</mmcif_mdb:publ_flag> <mmcif_mdb:value>110.9</mmcif_mdb:value> <mmcif_mdb:value_esd>0.2</mmcif_mdb:value_esd> </mmcif_mdb:geom_angle> <mmcif_mdb:geom_angle atom_site_id_1="O1" atom_site_id_2="C2" atom_site_id_3="O21" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <mmcif_mdb:publ_flag>yes</mmcif_mdb:publ_flag> <mmcif_mdb:value>122.2</mmcif_mdb:value> <mmcif_mdb:value_esd>0.3</mmcif_mdb:value_esd> </mmcif_mdb:geom_angle> <mmcif_mdb:geom_angle atom_site_id_1="C3" atom_site_id_2="C2" atom_site_id_3="O21" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <mmcif_mdb:publ_flag>yes</mmcif_mdb:publ_flag> <mmcif_mdb:value>127.0</mmcif_mdb:value> <mmcif_mdb:value_esd>0.3</mmcif_mdb:value_esd> </mmcif_mdb:geom_angle> <mmcif_mdb:geom_angle atom_site_id_1="C2" atom_site_id_2="C3" atom_site_id_3="N4" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <mmcif_mdb:publ_flag>yes</mmcif_mdb:publ_flag> <mmcif_mdb:value>101.3</mmcif_mdb:value> <mmcif_mdb:value_esd>0.2</mmcif_mdb:value_esd> </mmcif_mdb:geom_angle> <mmcif_mdb:geom_angle atom_site_id_1="C2" atom_site_id_2="C3" atom_site_id_3="C31" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <mmcif_mdb:publ_flag>yes</mmcif_mdb:publ_flag> <mmcif_mdb:value>111.3</mmcif_mdb:value> <mmcif_mdb:value_esd>0.2</mmcif_mdb:value_esd> </mmcif_mdb:geom_angle> <mmcif_mdb:geom_angle atom_site_id_1="C2" atom_site_id_2="C3" atom_site_id_3="H3" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <mmcif_mdb:publ_flag>no</mmcif_mdb:publ_flag> <mmcif_mdb:value>107</mmcif_mdb:value> <mmcif_mdb:value_esd>1</mmcif_mdb:value_esd> </mmcif_mdb:geom_angle> <mmcif_mdb:geom_angle atom_site_id_1="N4" atom_site_id_2="C3" atom_site_id_3="C31" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <mmcif_mdb:publ_flag>yes</mmcif_mdb:publ_flag> <mmcif_mdb:value>116.7</mmcif_mdb:value> <mmcif_mdb:value_esd>0.2</mmcif_mdb:value_esd> </mmcif_mdb:geom_angle> </mmcif_mdb:geom_angleCategory> An optional 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. An optional 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. An optional 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. An optional 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. An optional 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. An optional 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. An optional 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. An optional 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. An optional 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. An optional 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. An optional 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. An optional 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. An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. This code signals whether the angle is referred to in a publication or should be placed in a table of significant angles. Angle in degrees defined by the three sites _geom_angle.atom_site_id_1, _geom_angle.atom_site_id_2 and attribute atom_site_id_3 in category geom_angle. The standard uncertainty (estimated standard deviation) of attribute value in category geom_angle. The identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The identifier of the second of the three atom sites that define the angle. The second atom is taken to be the apex of the angle. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The symmetry code of the first of the three atom sites that define the angle. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 The symmetry code of the second of the three atom sites that define the angle. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 The symmetry code of the third of the three atom sites that define the angle. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 Data items in the GEOM_BOND category record details about the bond lengths as calculated from the contents of the ATOM, CELL and SYMMETRY data. Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <mmcif_mdb:geom_bondCategory> <mmcif_mdb:geom_bond atom_site_id_1="O1" atom_site_id_2="C2" site_symmetry_1="1_555" site_symmetry_2="1_555"> <mmcif_mdb:dist>1.342</mmcif_mdb:dist> <mmcif_mdb:dist_esd>0.004</mmcif_mdb:dist_esd> <mmcif_mdb:publ_flag>yes</mmcif_mdb:publ_flag> </mmcif_mdb:geom_bond> <mmcif_mdb:geom_bond atom_site_id_1="O1" atom_site_id_2="C5" site_symmetry_1="1_555" site_symmetry_2="1_555"> <mmcif_mdb:dist>1.439</mmcif_mdb:dist> <mmcif_mdb:dist_esd>0.003</mmcif_mdb:dist_esd> <mmcif_mdb:publ_flag>yes</mmcif_mdb:publ_flag> </mmcif_mdb:geom_bond> <mmcif_mdb:geom_bond atom_site_id_1="C2" atom_site_id_2="C3" site_symmetry_1="1_555" site_symmetry_2="1_555"> <mmcif_mdb:dist>1.512</mmcif_mdb:dist> <mmcif_mdb:dist_esd>0.004</mmcif_mdb:dist_esd> <mmcif_mdb:publ_flag>yes</mmcif_mdb:publ_flag> </mmcif_mdb:geom_bond> <mmcif_mdb:geom_bond atom_site_id_1="C2" atom_site_id_2="O21" site_symmetry_1="1_555" site_symmetry_2="1_555"> <mmcif_mdb:dist>1.199</mmcif_mdb:dist> <mmcif_mdb:dist_esd>0.004</mmcif_mdb:dist_esd> <mmcif_mdb:publ_flag>yes</mmcif_mdb:publ_flag> </mmcif_mdb:geom_bond> <mmcif_mdb:geom_bond atom_site_id_1="C3" atom_site_id_2="N4" site_symmetry_1="1_555" site_symmetry_2="1_555"> <mmcif_mdb:dist>1.465</mmcif_mdb:dist> <mmcif_mdb:dist_esd>0.003</mmcif_mdb:dist_esd> <mmcif_mdb:publ_flag>yes</mmcif_mdb:publ_flag> </mmcif_mdb:geom_bond> <mmcif_mdb:geom_bond atom_site_id_1="C3" atom_site_id_2="C31" site_symmetry_1="1_555" site_symmetry_2="1_555"> <mmcif_mdb:dist>1.537</mmcif_mdb:dist> <mmcif_mdb:dist_esd>0.004</mmcif_mdb:dist_esd> <mmcif_mdb:publ_flag>yes</mmcif_mdb:publ_flag> </mmcif_mdb:geom_bond> <mmcif_mdb:geom_bond atom_site_id_1="C3" atom_site_id_2="H3" site_symmetry_1="1_555" site_symmetry_2="1_555"> <mmcif_mdb:dist>1.00</mmcif_mdb:dist> <mmcif_mdb:dist_esd>0.03</mmcif_mdb:dist_esd> <mmcif_mdb:publ_flag>no</mmcif_mdb:publ_flag> </mmcif_mdb:geom_bond> <mmcif_mdb:geom_bond atom_site_id_1="N4" atom_site_id_2="C5" site_symmetry_1="1_555" site_symmetry_2="1_555"> <mmcif_mdb:dist>1.472</mmcif_mdb:dist> <mmcif_mdb:dist_esd>0.003</mmcif_mdb:dist_esd> <mmcif_mdb:publ_flag>yes</mmcif_mdb:publ_flag> </mmcif_mdb:geom_bond> </mmcif_mdb:geom_bondCategory> An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. The intramolecular bond distance in angstroms. The standard uncertainty (estimated standard deviation) of attribute dist in category geom_bond. This code signals whether the bond distance is referred to in a publication or should be placed in a list of significant bond distances. The identifier of the first of the two atom sites that define the bond. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The identifier of the second of the two atom sites that define the bond. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The symmetry code of the first of the two atom sites that define the bond. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 The symmetry code of the second of the two atom sites that define the bond. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 Data items in the GEOM_CONTACT category record details about interatomic contacts as calculated from the contents of the ATOM, CELL and SYMMETRY data. Example 1 - based on data set CLPHO6 of Ferguson, Ruhl, McKervey & Browne [Acta Cryst. (1992), C48, 2262-2264]. An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. The interatomic contact distance in angstroms. The standard uncertainty (estimated standard deviation) of attribute dist in category geom_contact. This code signals whether the contact distance is referred to in a publication or should be placed in a list of significant contact distances. The identifier of the first of the two atom sites that define the contact. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The identifier of the second of the two atom sites that define the contact. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The symmetry code of the first of the two atom sites that define the contact. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 The symmetry code of the second of the two atom sites that define the contact. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 Data items in the GEOM_HBOND category record details about hydrogen bonds as calculated from the contents of the ATOM, CELL and SYMMETRY data. Example 1 - based on C~14~H~13~ClN~2~O.H~2~O, reported by Palmer, Puddle & Lisgarten [Acta Cryst. (1993), C49, 1777-1779]. <mmcif_mdb:geom_hbondCategory> <mmcif_mdb:geom_hbond atom_site_id_A="OW" atom_site_id_D="N6" atom_site_id_H="HN6"> <mmcif_mdb:angle_DHA>169.6</mmcif_mdb:angle_DHA> <mmcif_mdb:dist_DA>2.801</mmcif_mdb:dist_DA> <mmcif_mdb:dist_DH>0.888</mmcif_mdb:dist_DH> <mmcif_mdb:dist_HA>1.921</mmcif_mdb:dist_HA> <mmcif_mdb:publ_flag>yes</mmcif_mdb:publ_flag> </mmcif_mdb:geom_hbond> <mmcif_mdb:geom_hbond atom_site_id_A="O7" atom_site_id_D="OW" atom_site_id_H="HO2"> <mmcif_mdb:angle_DHA>153.5</mmcif_mdb:angle_DHA> <mmcif_mdb:dist_DA>2.793</mmcif_mdb:dist_DA> <mmcif_mdb:dist_DH>0.917</mmcif_mdb:dist_DH> <mmcif_mdb:dist_HA>1.923</mmcif_mdb:dist_HA> <mmcif_mdb:publ_flag>yes</mmcif_mdb:publ_flag> </mmcif_mdb:geom_hbond> <mmcif_mdb:geom_hbond atom_site_id_A="N10" atom_site_id_D="OW" atom_site_id_H="HO1"> <mmcif_mdb:angle_DHA>179.7</mmcif_mdb:angle_DHA> <mmcif_mdb:dist_DA>2.842</mmcif_mdb:dist_DA> <mmcif_mdb:dist_DH>0.894</mmcif_mdb:dist_DH> <mmcif_mdb:dist_HA>1.886</mmcif_mdb:dist_HA> <mmcif_mdb:publ_flag>yes</mmcif_mdb:publ_flag> </mmcif_mdb:geom_hbond> </mmcif_mdb:geom_hbondCategory> The angle in degrees defined by the donor-, hydrogen- and acceptor-atom sites in a hydrogen bond. The standard uncertainty (estimated standard deviation) of attribute angle_DHA in category geom_hbond. An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. The distance in angstroms between the donor- and acceptor-atom sites in a hydrogen bond. The standard uncertainty (estimated standard deviation) in angstroms of attribute dist_DA in category geom_hbond. The distance in angstroms between the donor- and hydrogen-atom sites in a hydrogen bond. The standard uncertainty (estimated standard deviation) in angstroms of attribute dist_DH in category geom_hbond. The distance in angstroms between the hydrogen- and acceptor- atom sites in a hydrogen bond. The standard uncertainty (estimated standard deviation) in angstroms of attribute dist_HA in category geom_hbond. This code signals whether the hydrogen-bond information is referred to in a publication or should be placed in a table of significant hydrogen-bond geometry. The identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The symmetry code of the acceptor-atom site that defines the hydrogen bond. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 The symmetry code of the donor-atom site that defines the hydrogen bond. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 The symmetry code of the hydrogen-atom site that defines the hydrogen bond. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 Data items in the GEOM_TORSION category record details about torsion angles as calculated from the contents of the ATOM, CELL and SYMMETRY data. The vector direction attribute atom_site_id_2 in category geom_torsion to attribute atom_site_id_3 in category geom_torsion is the viewing direction, and the torsion angle is the angle of twist required to superimpose the projection of the vector between site 2 and site 1 onto the projection of the vector between site 3 and site 4. Clockwise torsions are positive, anticlockwise torsions are negative. Ref: Klyne, W. & Prelog, V. (1960). Experientia, 16, 521-523. Example 1 - based on data set CLPHO6 of Ferguson, Ruhl, McKervey & Browne [Acta Cryst. (1992), C48, 2262-2264]. An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. This code signals whether the torsion angle is referred to in a publication or should be placed in a table of significant torsion angles. The value of the torsion angle in degrees. The standard uncertainty (estimated standard deviation) of attribute value in category geom_torsion. The identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The symmetry code of the first of the four atom sites that define the torsion angle. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 The symmetry code of the second of the four atom sites that define the torsion angle. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 The symmetry code of the third of the four atom sites that define the torsion angle. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 The symmetry code of the fourth of the four atom sites that define the torsion angle. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 Data items in the JOURNAL category record details about the book-keeping by the journal staff when processing a data block submitted for publication. The creator of a data block will not normally specify these data. The data names are not defined in the dictionary because they are for journal use only. Example 1 - based on Acta Cryst. file for entry HL0007 [Willis, Beckwith & Tozer (1991). Acta Cryst. C47, 2276-2277]. <mmcif_mdb:journalCategory> <mmcif_mdb:journal entry_id="TOZ"> <mmcif_mdb:coden_ASTM>ACSCEE</mmcif_mdb:coden_ASTM> <mmcif_mdb:coeditor_code>HL0007</mmcif_mdb:coeditor_code> <mmcif_mdb:date_accepted>1991-04-18</mmcif_mdb:date_accepted> <mmcif_mdb:date_from_coeditor>1991-04-18</mmcif_mdb:date_from_coeditor> <mmcif_mdb:date_printers_first>1991-08-07</mmcif_mdb:date_printers_first> <mmcif_mdb:date_proofs_out>1991-08-07</mmcif_mdb:date_proofs_out> <mmcif_mdb:date_recd_electronic>1991-04-15</mmcif_mdb:date_recd_electronic> <mmcif_mdb:issue>NOV91</mmcif_mdb:issue> <mmcif_mdb:name_full>Acta Crystallographica Section C</mmcif_mdb:name_full> <mmcif_mdb:page_first>2276</mmcif_mdb:page_first> <mmcif_mdb:page_last>2277</mmcif_mdb:page_last> <mmcif_mdb:techeditor_code>C910963</mmcif_mdb:techeditor_code> <mmcif_mdb:volume>47</mmcif_mdb:volume> <mmcif_mdb:year>1991</mmcif_mdb:year> </mmcif_mdb:journal> </mmcif_mdb:journalCategory> Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the JOURNAL_INDEX category are used to list terms used to generate the journal indexes. The creator of a data block will not normally specify these data items. Example 1 - based on a paper by Zhu, Reynolds, Klein & Trudell [Acta Cryst. (1994), C50, 2067-2069]. <mmcif_mdb:journal_indexCategory> <mmcif_mdb:journal_index term="C16H19NO4" type="O"> <mmcif_mdb:subterm></mmcif_mdb:subterm> </mmcif_mdb:journal_index> <mmcif_mdb:journal_index term="alkaloids" type="S"> <mmcif_mdb:subterm>(-)-norcocaine</mmcif_mdb:subterm> </mmcif_mdb:journal_index> <mmcif_mdb:journal_index term="(-)-norcocaine" type="S"> <mmcif_mdb:subterm></mmcif_mdb:subterm> </mmcif_mdb:journal_index> <mmcif_mdb:journal_index term=" [2R,3S-(2\b,3\b)]-methyl 3-(benzoyloxy)-8-azabicyclo[3.2.1]octane-2-carboxylate" type="S"> <mmcif_mdb:subterm></mmcif_mdb:subterm> </mmcif_mdb:journal_index> </mmcif_mdb:journal_indexCategory> Journal index data items are defined by the journal staff. Journal index data items are defined by the journal staff. Journal index data items are defined by the journal staff. Data items in the MDB_ALIGN_SEARCH_PARAM category give details of template search. This data item is a pointer to attribute id in category entity in the ENTITY category. A flag to indicate whether a filter was used during database searches. Reference to the filter used during database searches. blast default filter DUST Short description of the alignment scoring techinque used to compare sequences. blastp high score Substitution matrix used for sequence comparison. BLOSUM62 Supplementary information about parameters used during template searches. This data item is a pointer to attribute id in category mdb_list_align_method in the MDB_LIST_ALIGN_METHOD category. This data item is a pointer to attribute id in category mdb_model in the MDB_MODEL category. Data items in MDB_ALIGN_TEMPLATES category store information about all templates identified for all models using different methods. 'yes' indicates that this template was used in the modelling procedure, 'no' that it was not utilized to build the model. This data item is a pointer to attribute id in category entity in the ENTITY category. Percentage of identity between the template (_mdb_align_templates.id) and the target (_mdb_align_templates.mod_id) sequences. Probability value for the alignment template-target. Residual factor R for reflections that satisfy the resolution limits established by attribute ls_d_res_high in category refine and attribute ls_d_res_low in category refine and the observation limit established by attribute observed_criterion in category reflns, and that were used as the test (i.e., excluded from refinement) reflections when refinement included calculation of a "free" R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details. in category reflns sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure factor amplitudes F~calc~ = the calculated structure factor amplitudes sum is taken over the specified reflections Residual factor R for reflections that satisfy the resolution limits established by attribute ls_d_res_high in category refine and attribute ls_d_res_low in category refine and the observation limit established by attribute observed_criterion in category reflns, and that were used as the working (i.e., included in refinement) reflections when refinement included calculation of a "free" R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details. in category reflns attribute ls_R_factor_obs in category refine should not be confused with attribute ls_R_factor_R_work in category refine, the former reports the results of a refinement in which all observed reflections were used, the latter a refinement in which a subset of the observed reflections were excluded from refinement for the calculation of a "free" R factor. However, it would be meaningful to quote both values if a "free" R factor were calculated for most of the refinement, but all of the observed reflections were used in the final rounds of refinement, such a protocol should be explained in attribute details. in category refine sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure factor amplitudes F~calc~ = the calculated structure factor amplitudes sum is taken over the specified reflections Residual factor R for all reflections that satisfy the resolution limits established by attribute ls_d_res_high in category refine and attribute ls_d_res_low. in category refine sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure factor amplitudes F~calc~ = the calculated structure factor amplitudes sum is taken over the specified reflections The highest resolution in angstroms for the interplanar spacing in the reflection data used in refinement. This is the smallest d value. The lowest resolution in ansgtroms for the interplanar spacing in the reflection data used in refinement. This is the largest d value. Score value for the alignement template-target in accordance to _mdb_align_search_param.score_ref or _mdb_align_thread_param.score_ref data items. This data item is a pointer to attribute id in category mdb_list_align_method in the MDB_LIST_ALIGN_METHOD category. This data item is a pointer to attribute id in category mdb_model in the MDB_MODEL category. This data item is a pointer to attribute id in category mdb_list_template in the MDB_LIST_TEMPLATE category. Data items in the MDB_ALIGN_THREAD_PARAM category give details of template search. Type of alignement: global or local used to compare different sequences. This data item is a pointer to attribute id in category entity in the ENTITY category. Fold library. Gap introduction penality. Gap extention penality. Any additional parameter used in the evaluation of the fold (e.g. contact potential). Weight term in the fold match for the paramater in attribute param in category mdb_align_thread_param. Alignment score technique. blastp high score Sequence weight term in the fold match. Scondary structure weight term in the fold match. Supplementary information about parameters used during template searches. This data item is a pointer to attribute id in category mdb_list_align_method in the MDB_LIST_ALIGN_METHOD category. This data item is a pointer to attribute id in category mdb_model in the MDB_MODEL category. Data items in the MDB_AUDIT category record details about the creation and subsequent revisions of the data block. Date at which the data block is created (corresponding to attribute revision_level in category mdb_audit equal to 0) or modified (corresponding to attribute revision_level in category mdb_audit greater than 0). 1999-12-08 Name identifying the curator. em333 A record of any changes in the data block. Name of the software used to load entry. mdbloaderv013.pl User name. dataloader The value of attribute revision_level in category mdb_audit must uniquely identify a record in the MDB_AUDIT list. attribute revision_level in category mdb_audit equal to 0 corresponds to the initial version of the data while attribute revision_level in category mdb_audit greater than 0 corresponds to the subsequent revisions. 0 Category MDB_BIOL_PDB_CMP holds data from the PDB COMPND record. Introduced for direct compatibility with PDB and should be used only for data converted from the PDB format. BIOLOGICAL_UNIT If the MOLECULE functions as part of a larger biological unit, the entire functional unit may be described. CHAIN Comma-separated list of chain identifier(s). "NULL" is used to indicate a blank chain identifier. OTHER_DETAILS Additional comments. ENGINEERED Indicates that the molecule was produced using recombinant technology or by purely chemical synthesis. FRAGMENT Specifies a domain or region of the molecule. MOLECULE Name of the macromolecule. MUTATION Describes mutations from the wild type molecule. SYNONYM Comma-separated list of synonyms for the MOLECULE. This data item is a pointer to attribute id in category struct_biol in STRUCT_BIOL category. EC The Enzyme Commission number associated with the molecule. _mdb_biol_PDB_cmp.ec is a pointer to _mdb_mpw_ec_list.ec_code Category MDB_BIOL_PDB_SRC holds data from the PDB SOURCE record. Introduced for direct compatibility with PDB and should be used only for data converted from the PDB format. ATCC American Type Culture Collection tissue culture number. CELL Identifies the particular cell type. CELL_LINE The specific line of cells used in the experiment. CELLULAR_LOCATION Identifies the location inside (or outside) the cell. ORGANISM_COMMON Common name of the organism. OTHER_DETAILS Used to present information on the source which is not given elsewhere. EXPRESSION_SYSTEM System used to express recombinant macromolecules. EXPRESSION_SYSTEM_ATCC_NUMBER Identifies the ATCC number of the expression system EXPRESSION_SYSTEM_CELL Specific cell type which expressed the molecule. EXPRESSION_SYSTEM_CELL_LINE The specific line of cells used as the expression system. EXPRESSION_SYSTEM_CELLULAR_LOCATION Identifies the location inside or outside the cell which expressed the molecule. EXPRESSION_SYSTEM_GENE Name of the gene used in recombinant experiment. EXPRESSION_SYSTEM_ORGAN Specific organ which expressed the molecule. EXPRESSION_SYSTEM_ORGANELLE Specific organelle which expressed the molecule. EXPRESSION_SYSTEM_PLASMID Plasmid used in the recombinant experiment. EXPRESSION_SYSTEM_STRAIN Strain of the organism in which the molecule was expressed. EXPRESSION_SYSTEM_TISSUE Specific tissue which expressed the molecule. EXPRESSION_SYSTEM_VARIANT Variant of the organism used as the expression system. EXPRESSION_SYSTEM_VECTOR Identifies the vector used. EXPRESSION_SYSTEM_VECTOR_TYPE Identifies the type of vector used, i.e., plasmid, virus, or cosmid. FRAGMENT A domain or fragment of the molecule may be specified. GENE Identifies the gene. ORGAN Organized group of tissues that carries on a specialized function. ORGANELLE Organized structure within a cell. PLASMID Identifies the plasmid containing the gene. ORGANISM_SCIENTIFIC Scientific name of the organism. SECRETION Identifies the secretion, such as saliva, urine, or venom, from which the molecule was isolated. STRAIN Identifies the strain. SYNTHETIC Indicates a chemically-synthesized source. TISSUE Organized group of cells with a common function and structure. VARIANT Identifies the variant. This data item is a pointer to attribute id in category struct_biol in STRUCT_BIOL category. Data items in the MDB_DB_LIST category store information on the database modules corresponding to specific dictinaries or dictionary extensions. Information on the database module / dictionary extension. Database module / dictionary extension identifier. This is a unique identifier. Note that this item need not be a number. Data items in the MDB_DEPOSITION category record details about deposition source. Flag indicating automatic deposition. Flag indicating to which database the entry belongs. This item is a child of attribute db_id in category mdb_db_list. Flag indicating external (ext) or internal (int) deposition. Short description of the source or origin of the entry. SWISS-MODEL (Automated Protein Modelling Server) This data is a pointer to attribute id in category entry in the ENTRY category. Data items in the MDB_DYNAMICS category store information about the application of molecular dynamics simulations for each step. Boundary condition details. Boundary extention from the furthermost dimension of the modelled molecule in the X direction. Boundary extention from the furthermost dimension of the modelled molecule in the Y direction. Boundary extention from the furthermost dimension of the modelled molecule in the Z direction. Type of charges used. Constraints applied during dynamics simulation. Type of function used to define constraints applied during dynamics simulation. This data item is a pointer to attribute id in category entity in the ENTITY category. This data item is a pointer to attribute id in category mdb_force_field in the category MDB_FORCE_FIELD. Dynammics technique. Langevin constant temperature constant pressure This data item is a pointer to attribute id in category mdb_model in the MDB_MODEL category. This data item is a pointer to attribute id in category mdb_model_struc_seg in the MDB_MODEL_STRUC_SEG category. Length of the simulation. Flag indicating if a solvent model was used. This data item is a pointer to attribute id in category mdb_solvent in the MDB_SOLVENT category. Additional information on the applied constraints. Temperature control model. velocity scaling Berendsen temperature bath Nose-Hoover dynamics Starting temperature. Ending temperature. Integration time step for the simulation (dt). The value of attribute step_id in category mdb_dynamics must uniquely identify each step of molecular dynamics for each attribute seg_id. in category mdb_dynamics Note that this item need not be a number it can be any unique identifier of each molecular dynamics step. Data items in the MDB_ENERGY_MIN category specify parameters used during the energy minimisation. This data item shows if the energy minimisation is conducted using the united atom approximation or all atoms. Type of charges. Constraints applied during energy minimisation. Type of function used to define constraints applied during energy minimisation. Additional information on the applied constraints. Convergence criterion based on the change in coordinates (displacement) between successive steps. Number of minimisation cycles allowed. Dielectric constant. Dielectric function. Convergence criterion based on the energy difference between successive steps. This data item is a pointer to attribute id in category entity in the ENTITY category. This data item is a pointer to attribute id in category mdb_force_field in the category MDB_FORCE_FIELD. Root mean square gradient convergence criterion. Minimisation technique. steepest descent conjugate gradient Newton-Raphson This data item is a pointer to attribute id in category mdb_model in the MDB_MODEL category. Distance cutoff for non bonded interaction. pH value used to protonate residues. This data item is a pointer to attribute id in category mdb_model_struc_seg in the MDB_MODEL_STRUC_SEG category. Flag indicating if a solvent model was used. This data item is a pointer to attribute id in category mdb_solvent in the MDB_SOLVENT category. The value of attribute step_id in category mdb_energy_min must uniquely identify each minimisation step for each attribute seg_id. in category mdb_energy_min Note that this item need not be a number it can be any unique identifier of each minimisation event. Data items in the category MDB_ENTITY_SEQ_CD record details about the codon sequence such as reference to the original gene, the database containing the sequence, the identification code, the accession code and the URL of the database. Flag to indicate if the codon sequence was submitted by the author(s) or genereted by MDB. URL of the database containing the gene encoding the amino acid sequence of an entity. Accession number of the gene encoding the amino acid sequence of an entity. This data item holds the creation date of reference file. Database containing the gene encoding the amino acid sequence of an entity. Genbank Genbank Nucleic Acid Database NDB Short description of the gene encoding the amino acid sequence of an entity. Identification code of the gene encoding the amino acid sequence of an entity. This data item is a pointer to attribute id in category entity in the ENTITY category. Data items in the category MDB_ENTITY_SEQ_MON record details about the monomer sequence such as reference to the original name, the database containing the sequence, the identification code, the accession code and the URL. This data item is a pointer to attribute id in category entity in the ENTITY category. URL of the database containing the polymeric entity. Accession number of the polymeric entity. This data item refers to the creation date of reference file. Short description of the polymeric entity. Database containing the polymeric entity. Swiss Prot SWP Nucleic Acid Database NDB Protein Data Bank PDB Identification code of the polymeric entity. Data items in the category MDB_ENTITY_SEQ_MOTIF record details about the motif(s) and motif identification method(s). This data item defines the residue number with which the motif begins in the entity, according to the full sequence of attribute num. in category entity_poly_seq This data item is a pointer to attribute num in category entity_poly_seq in the ENTITY_POLY_SEQ category. Short description of the motif. This data item defines the residue number with which the motif ends in the entity, according to the full sequence of attribute num. in category entity_poly_seq This data item is a pointer to attribute mon_num in category sequence in the ENTITY_POLY_SEQ category. This data item is a pointer to attribute id in category entity in the ENTITY category. Library of motifs or patterns on which the search was done. Method used to identify a motif. Monomer sequence of the motif. The value of attribute id in category mdb_entity_seq_motif must uniquely identify a record in the MDB_ENTITY_SEQ_MOTIF list. Note that this item need not be a number, it can be any unique identifier. Data items in the MDB_ENTITY_SEQ_RELATE category record references to closely related polymeric entities and/or to the wild polymeric entity in case of a mutated sequence. Short description of the differences between related entities. Flag to indicate if the codon sequence was submitted by the author(s) or genereted by MDB. This data item is a pointer to attribute id in category entity in the ENTITY category. URL of the database containing the entity closely related to the entity described in attribute entity_id in category mdb_entity_seq_relate. Accession number of a sequence/entity closely related to the main entity(ies) described in entity_id. Entry creation date of a sequence/entity closely related to the main entity(ies) described in entity_id. Short description of a sequence/entity closely related to the main entity(ies) described in entity_id. Database containing the sequence/entity closely related to the main entity(ies) described in entity_id. Swiss Prot SWP Nucleic Acid Database NDB Protein Data Bank PDB Identification code of a sequence/entity closely related to the main entity(ies) described in entity_id. Data items in the MDB_EXT_LOC_LIST category hold locations of the database objects stored outside of the tablespaces, e.g. BFILES. Information on the external object. External storage identifier. This is a unique identifier. Note that this item need not be a number. External storage file name. Database module / dictionary extension identifier. This item is a child of attribute db_id in category mdb_db_list. External storage directory alias. Data items in the MDB_FORCE_FIELD category specify the force field used for energy calculations, the version and the possible modifications. 'yes' indicates that modifications were applied to the original force field, 'no' that no modifications were applied. Force field name. AMBER GROMOS CHARMM Short description of the modified or added parameters. Force field version. 1.4 23 The value of attribute id in category mdb_force_field must uniquely identify a record in the MDB_FORCE_FIELD list. Note that this item need not be a number, it can be any unique identifier. In the MDB_LIST_ALIGN_METHOD category contains a list of all the methods used to find templates. Procedure used to find templates. FASTA Reference or additional information for the threading algorithm. Supplementary information on procedures used to find templates. The value of attribute id in category mdb_align_method must uniquely identify a method used to find templates. Note that this item need not be a number, it can be any unique identifier. Data items in MDB_LIST_TEMPLATE category store a complete list of all templates identified for all models. Some templates can be not applied for modelling. This data item is a pointer to attribute id in category entity in the ENTITY category. This data item is a pointer to attribute id in category mdb_model in the MDB_MODEL category. Creation date date of the template entry in the reference database. 1998-12-24 1996-01-06 Name of the database containing the template entry. PDB CSD Genbank Short description of the template in the reference database. Identification code of the template in the reference database. 1ABC 1PHK Accession code of the template in the Swiss-Prot database. Q02145 POO212 The value of attribute id in category mdb_list_template must uniquely identify a template. Note that this item need not be a number, it can be any unique identifier. Data items in the MDB_MODEL category give details (such as the first and the end residue, etc.) about each model. This data item defines a residue number with which the model begins, according to the full sequence numbering as in attribute num. in category entity_poly_seq This data item is a pointer to attribute mon_num in category sequence in the ENTITY_POLY_SEQ category. This data item defines the residue number with which model ends, according to the full sequence numbering (according to attribute num). in category entity_poly_seq This data item is a pointer to attribute mon_num in category sequence in the ENTITY_POLY_SEQ category. This data item is a pointer to attribute id in category entity in the ENTITY category. A method used to produce the model. This item holds description of a method or software used in modelling. The value of attribute id in category mdb_model must uniquely identify a record in the MDB_MODEL list. Note that this item need not be a number, it can be any unique identifier. The category mdb_model_eval stores evaluation data of the reliability (accuracy) of the model structure. Flag to indicate if data items in the category MDB_MODEL_EVAL are submitted by the author(s) of this datablock or genereted by MDB. This data item is a pointer to attribute id in category entity in the ENTITY category. This data item is a genereted parameter based on a probability function. The evaluation of the model is computed as: #need to be revised, dummy range values used! This data item is a pointer to attribute id in category mdb_model in the MDB_MODEL category. Model building procedure for segments in models, there can be more than one segment per model. This data item defines the residue number with which the segment begins, according to the full sequence numbering attribute num. in category entity_poly_seq This data item is a pointer to attribute num in category entity_poly_seq in the ENTITY_POLY_SEQ category. This data item shows if the segement is modelled from a parent structure(s), databse search, or generated de novo. This data item shows if the segment is defined as a structurally conserved or variable region, or undefined. This data item gives details of the model building. This data item defines the residue number with which the segment ends, according to the full sequence numbering attribute num. in category entity_poly_seq 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 entity in the ENTITY category. This data item is a pointer to attribute method_id in category mdb_model_param in the MDB_MODEL_PARAM category. This data item is a pointer to attribute id in category mdb_model in the MDB_MODEL category. This data item shows the type of template used for the segment single template, multiple templates, or averaged from multiple template structure. This data item shows the segment attribution i.e. backbone or side chains or both. The value of attribute id in category mdb_model_proc_seg must uniquely identify a record in the MDB_MODEL_PROC_SEG list. Note that this item need not be a number, it can be any unique identifier. Date items in the MDB_MODEL_STRUCT category record details of definition, description and quality for each model on a residue basis level. Confidence factor per residue. The Model C-factor is computed as: 50.0 * (1/ number selected templates) and 100.0 for all atoms added during loop and side-chain building. #need to revise! Estimation of the bond angles accuracy on a residue level. #need to revise, dummy range values used! Estimation of the bonds accuracy on a residue level. #need to revise, dummy range values used! Estimation of the torsion angles accuracy on a residue level residue. #need to revise, dummy range values used! Conservation probability in the alignment (at a monomer level). Consensus sequence for the alignment with template(s) (at a monomer level). Type of alignment match for each residue in the alignment with template(s). Solvent accessibility associated with each residue. More information on solvent accessibility (used criteria and model) are found in the category MDB_MODEL_STRUCT_ASA. This data item is a pointer to attribute id in category entity in the ENTITY category. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. Secondary structure associated with each residue. More information on secondary structure (criteria and model) can be found in the category MDB_MODEL_STRUCT_SS. 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 mdb_model in the MDB_MODEL category. Data items in the mdb_model_struct_asa category specify accessibility calculations / prediction details. This data item defines if the accessibility was assigned from the three dimensional structure or predicted. Algorithm used to assign / predict the solvent accssibility. Short description of the model and technique used to assign / predict accessibility. This data item is a pointer to attribute id in category entity in the ENTITY category. Model used to assign / predict the solvent accessibility. This data item is a pointer to attribute id in category mdb_model in the MDB_MODEL category. Data items in the mdb_model_struct_fold category record details about the model fold. Fold identification mode: predicted or assigned. The algorithm used to characterise the folding. This data item is a pointer to attribute id in category entity in the ENTITY category. Fold class of the model. all beta proteins all alpha proteins alpha plus beta proteins Family to which the fold of the model belongs. serine/threonin kinases hemopexin-like domain HMG-box Superfamily to which the fold of the model belongs. protein kinases hemopexin-like domain HMG-box The topology of folding adopted by the model. thioredoxin fold beta barrel beta sandwich The URL that localizes the reference database. pdb.ccdc.cam.ac.uk This data item is a pointer to attribute id in category mdb_model in the MDB_MODEL category. An abbreviation that identifies the reference database. Structural Classification of Proteins SCOP Data items in the MDB_MODEL_STRUCT_SRC category specify the source of some data items present in the MDB_MODEL_STRUCT category. These data items can be submitted by the author(s) of the model/entry or generated automatically by MDB. SD stands for submitted data and GD for generated data. Flag indicating if the bond angle accuracy values were submitted by the author(s) or genereted by MDB. Flag indicating if the bond length accuracy values were submitted by the author(s) or genereted by MDB. Flag indicating if the torsion angle accuracy values were submitted by the author(s) or genereted by MDB. Flag indicating if the consensus sequence was submitted by the author(s) or genereted by MDB. Flag indicating if the alignment match value was submitted by the author(s) or genereted by MDB. Flag indicating if the alignment probability values were submitted by the author(s) or genereted by MDB. Flag indicating if the solvent accessibility prediction was submitted by the author(s) or genereted by MDB. This data item is a pointer to attribute id in category entity in the ENTITY category. Flag indicating if the secondary structure prediction was submitted by the author(s) or genereted by MDB. This data item is a pointer to attribute id in category mdb_model in the MDB_MODEL category. Data items in the mdb_model_struct_ss category specify secondary structure assignement details. This data item defines if the secondary structure was assigned from the three dimensional structure or predicted. Algorithm used to predict / assign the secondary structure. Short description of the model and technique used to assign / predict secondary structure. This data item is a pointer to attribute id in category entity in the ENTITY category. Assignment / prediction model. HEX HETX This data item is a pointer to attribute id in category mdb_model in the MDB_MODEL category. Data items in the category MDB_MPW_EC hold data of the MPW charts classified by EC numbers. Chart file name. 1.1.1.21 XYLXOL.CAT Reaction id in chart. AGLSETL.CAT R1 EC code of enzyme. _mdb_mpw_ec.ec_code is a pointer to _mdb_mpw_ec_list.ec_code AGLSETL.CAT 1.1.1.1 Category MDB_MPW_EC_LIST holds Enzyme Committee Nomenclature EC numbers. Systematic name of enzyme. 1.1.1.1 Alcohol dehydrogenase Enzyme Committee Nomenclature EC code. The value of attribute ec_code in category mdb_mpw_ec_list is a unique identifier. Data items in this category store information on multiple alignments of templates and targets. This data item is a pointer to attribute id in category entity in the ENTITY category. Number of positions in the alignment (length) including gaps for each model. This data item is a pointer to attribute id in category mdb_model in the MDB_MODEL category. Total number of aligned sequences (target and templates) for each model. Visual representation of the multiple alignment including gaps for each model. The value of attribute align_num in category mdb_multalign must uniquely identify a record in the MDB_MULTALIGN category. It is the number identifying each alignement. Note that this item needs to be a number. Data items in the MDB_MULTALIGN_ALIGN category contain the aligned sequences. This data item is a pointer to attribute id in category mdb_model in the MDB_MODEL category. Monomer sequence for target and template(s) including gaps which are identified as '-'. This data item is a pointer to attribute id in category mdb_list_template in the MDB_LIST_TEMPLATE category. This data item must uniquely and sequentially identify the monomer and gap positions for each alignment. This data item is a pointer to attribute align_num in category mdb_multalign in the MDB_MULTALIGN category. This data item must uniquely and sequentially (target, first template, second template, ect.) identify the target and template sequences for each alignment. The MDB_MULTALIGN_MATRIX category provides placeholders for transformation matrices and vectors of each template, describing transformations from initial coordinates to final coordinates in the multiple alignment superposition. This data item is a pointer to attribute id in category entity in the ENTITY category. The [1][1] element of the transformation matrix. The [1][2] element of the transformation matrix. The [1][3] element of the transformation matrix. The [2][1] element of the transformation matrix. The [2][2] element of the transformation matrix. The [2][3] element of the transformation matrix. The [3][1] element of the transformation matrix. The [3][2] element of the transformation matrix. The [3][3] element of the transformation matrix. The [1] element of the transformation vector. The [2] element of the transformation vector. The [3] element of the transformation vector. This data item is a pointer to attribute id in category mdb_model in the MDB_MODEL category. This data item is a pointer to attribute id in category mdb_list_template in the MDB_LIST_TEMPLATE category. Data items in the category MDB_SOLVED_STRUCTURE hold details of structures solved experimentally corresponding to models in MDB. Flag to indicate if data items in the category MDB_SOLVED_STRUCTURE are submitted by the author(s) of this datablock or genereted by MDB. This data item is a pointer to attribute id in category entity in the ENTITY category. 'yes' indicates that there is a experimentally solved structure, 'no' that there is no experimentally solved structure. URL of the database containing the solved structure. Entry creation date of the solved structure. Database containing the solved structure. Nucleic Acid Database NDB Protein Data Bank PDB Short description. Identification code of the solved structure. Swiss Prot accession code of the polymeric entity of the solved structure. Time flag related to model submission. This data item is a pointer to attribute id in category mdb_model in the MDB_MODEL category. Data items in the MDB_SOLVENT category store information on the solvent. Model used to simulate the solvent: explicit or continuum. Short description or publication reference for the used model. Specific model used to simulate the solvent. SPC TIP3P TIP4P ST2 Type of solvent used (e.g. water). The value of attribute id in category mdb_model must uniquely identify a record in the MDB_SOLVENT list. Note that this item need not be a number, it can be any unique identifier. The category mdb_submission serves to bind entry_id for each model submission to an integer key used to identify separate submissions (entries) in the data stored in other categories. The category also stores flat CIF file location for each entry. This item holds CIF flat file location for entry_id. This item is a pointer to attribute id in category entry in the category entry. Category MDB_SWP_AC_LIST holds the accession code of Swiss Prot database. Flag that identifies the primary Swiss Prot accession code. Swiss Prot accession code.It provides a stable way of identifying Swiss Prot entries from release to release. P12520 This data item is a pointer to attribute id in category mdb_swp_id_list in the MDB_SWP_ID_LIST category. Category MDB_SWP_DATA holds some fields of Swiss Prot database in relation to the PDB/MDB entry. Short description of the stored sequence. Organism(s) which was the source of the stored sequence. Percentage of identity between the sequence stored in the category entity_poly_seq and the sequence stored in Swiss Prot database. EC code for the sequence stored in Swiss Prot database. This data item is a pointer to attribute ec_code in category mdb_mpw_ec_list in the MDB_MPW_EC_LIST 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 id in category mdb_swp_id_list in the MDB_SWP_DATA category. Category MDB_SWP_ID_LIST holds the identification line of Swiss Prot database. Swiss Prot entry name of the sequence. First item of the identification line. VPR_HV1N5 Data items in the PHASING category record details about the phasing of the structure, listing the various methods used in the phasing process. Details about the application of each method are listed in the appropriate subcategories. Example 1 - hypothetical example. <mmcif_mdb:phasingCategory> <mmcif_mdb:phasing method="mir"></mmcif_mdb:phasing> <mmcif_mdb:phasing method="averaging"></mmcif_mdb:phasing> </mmcif_mdb:phasingCategory> A listing of the method or methods used to phase this structure. phasing by ab initio methods abinitio phase improvement by averaging over multiple images of the structure averaging phasing by direct methods dm phasing by iterative single-wavelength anomalous scattering isas phasing by iterative single-wavelength isomorphous replacement isir phasing beginning with phases calculated from an isomorphous structure isomorphous phasing by multiple-wavelength anomalous dispersion mad phasing by multiple isomorphous replacement mir phasing by multiple isomorphous replacement with anomalous scattering miras phasing by molecular replacement mr phasing by single isomorphous replacement sir phasing by single isomorphous replacement with anomalous scattering siras Data items in the PHASING_MAD category record details about the phasing of the structure where methods involving multiple-wavelength anomalous-dispersion techniques are involved. Example 1 - based on a paper by Shapiro et al. [Nature (London) (1995), 374, 327-337]. <mmcif_mdb:phasing_MADCategory> <mmcif_mdb:phasing_MAD entry_id="NCAD"></mmcif_mdb:phasing_MAD> </mmcif_mdb:phasing_MADCategory> A description of special aspects of the MAD phasing. A description of the MAD phasing method used to phase this structure. Note that this is not the computer program used, which is described in the SOFTWARE category, but rather the method itself. This data item should be used to describe significant methodological options used within the MAD phasing program. This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the PHASING_MAD_CLUST category record details about a cluster of experiments that contributed to the generation of a set of phases. Example 1 - based on a paper by Shapiro et al. [Nature (London) (1995), 374, 327-337]. <mmcif_mdb:phasing_MAD_clustCategory> <mmcif_mdb:phasing_MAD_clust expt_id="1" id="4 wavelength"> <mmcif_mdb:number_set>4</mmcif_mdb:number_set> </mmcif_mdb:phasing_MAD_clust> <mmcif_mdb:phasing_MAD_clust expt_id="1" id="5 wavelength"> <mmcif_mdb:number_set>5</mmcif_mdb:number_set> </mmcif_mdb:phasing_MAD_clust> <mmcif_mdb:phasing_MAD_clust expt_id="2" id="5 wavelength"> <mmcif_mdb:number_set>5</mmcif_mdb:number_set> </mmcif_mdb:phasing_MAD_clust> </mmcif_mdb:phasing_MAD_clustCategory> The number of data sets in this cluster of data sets. This data item is a pointer to attribute id in category phasing_MAD_expt in the PHASING_MAD_EXPT category. The value of attribute id in category phasing_MAD_clust must, together with attribute expt_id in category phasing_MAD_clust, uniquely identify a record in the PHASING_MAD_CLUST list. Note that this item need not be a number; it can be any unique identifier. Data items in the PHASING_MAD_EXPT category record details about a MAD phasing experiment, such as the number of experiments that were clustered together to produce a set of phases or the statistics for those phases. Example 1 - based on a paper by Shapiro et al. [Nature (London) (1995), 374, 327-337]. <mmcif_mdb:phasing_MAD_exptCategory> <mmcif_mdb:phasing_MAD_expt id="1"> <mmcif_mdb:R_normal_all>0.063</mmcif_mdb:R_normal_all> <mmcif_mdb:R_normal_anom_scat>0.451</mmcif_mdb:R_normal_anom_scat> <mmcif_mdb:delta_delta_phi>58.5</mmcif_mdb:delta_delta_phi> <mmcif_mdb:delta_phi_sigma>20.3</mmcif_mdb:delta_phi_sigma> <mmcif_mdb:mean_fom>0.88</mmcif_mdb:mean_fom> <mmcif_mdb:number_clust>2</mmcif_mdb:number_clust> </mmcif_mdb:phasing_MAD_expt> <mmcif_mdb:phasing_MAD_expt id="2"> <mmcif_mdb:R_normal_all>0.051</mmcif_mdb:R_normal_