International
Tables for Crystallography Volume G Definition and exchange of crystallographic data Edited by S. R. Hall and B. McMahon © International Union of Crystallography 2006 |
International Tables for Crystallography (2006). Vol. G. ch. 3.6, pp. 162-163
Section 3.6.6.3.1. Individual reflections
P. M. D. Fitzgerald,a* J. D. Westbrook,b P. E. Bourne,c B. McMahon,d K. D. Watenpaughe and H. M. Bermanf
a
Merck Research Laboratories, Rahway, New Jersey, USA,bProtein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, New Jersey, USA,cResearch Collaboratory for Structural Bioinformatics, San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0537, USA,dInternational Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, England,eretired; formerly Structural, Analytical and Medicinal Chemistry, Pharmacia Corporation, Kalamazoo, Michigan, USA, and fProtein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, New Jersey, USA |
The data items in these categories are as follows:
The bullet () indicates a category key. Where multiple items within a category are marked with a bullet, they must be taken together to form a compound key. The arrow (
) is a reference to a parent data item. Items in italics have aliases in the core CIF dictionary formed by changing the full stop (.) to an underscore (_) except where indicated by the
symbol.
Data items in the REFLN category are used in the same way in the mmCIF and core CIF dictionaries, and Section 3.2.3.2.1
can be consulted for details. However, in macromolecular crystallography it is not usual for reflection intensities to be given in units of electrons (the units specified by the core CIF dictionary). Thus it was necessary to introduce in the mmCIF dictionary data items for the magnitudes of structure factors and their A and B components in arbitrary units (Example 3.6.6.12
). A figure of merit ( _refln.fom) can also be included for reflections that were phased using experimental methods.
Example 3.6.6.12. Part of the reflection list for an HIV-1 protease structure (PDB 5HVP) described with data items in the REFLN category.
The REFLN_SYS_ABS category allows the intensities of the reflections that should be systematically absent to be tabulated. The ratio of the intensity to its standard uncertainty, given in the data item _refln_sys_abs.I_over_sigmaI, can be used to assess whether the reflection is indeed absent. The decision as to whether it is absent is left to the user of the mmCIF and is not recorded in the mmCIF.