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)\%, \q scan rate 1.2\% 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., "SHELX-76: structure determination and
refinement program", 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% 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_