International
Tables for
Crystallography
Volume G
Definition and exchange of crystallographic data
Edited by S. R. Hall and B. McMahon

International Tables for Crystallography (2006). Vol. G, ch. 3.6, pp. 162-164

Section 3.6.6.3. Reflection measurements

P. M. D. Fitzgerald,a* J. D. Westbrook,b P. E. Bourne,c B. McMahon,d K. D. Watenpaughe and H. M. Bermanf

aMerck 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
Correspondence e-mail:  paula_fitzgerald@merck.com

3.6.6.3. Reflection measurements

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The categories describing the reflections used in the refinement are as follows:

REFLN group
Individual reflections (§3.6.6.3.1[link])
 REFLN
 REFLN_SYS_ABS
Groups of reflections (§3.6.6.3.2[link])
 REFLNS
 REFLNS_SCALE
 REFLNS_SHELL
 REFLNS_CLASS

Data items in the REFLN category can be used to give information about the individual reflections that were used to derive the final model. The related category REFLN_SYS_ABS allows the reflections that should be systematically absent for the space group in which the structure was refined to be tabulated. Data items in the REFLNS category can be used to record information that applies to all of the reflections. Scale factors can be listed in the REFLNS_SCALE category, while the data items in REFLNS_SHELL can be used to record information about the reflection set by shells of resolution. The core CIF dictionary category REFLNS_CLASS, which can be used for a general classification of reflection groups according to criteria other than resolution shell, is not expected to be used in mmCIF applications.

3.6.6.3.1. Individual reflections

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The data items in these categories are as follows:

(a) REFLN [Scheme scheme76]

(b) REFLN_SYS_ABS [Scheme scheme79]

The bullet ([\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 ([\rightarrow]) 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 [\sim] 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[link] 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[link]). 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.

[Scheme scheme77]

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.

3.6.6.3.2. Groups of reflections

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The data items in these categories are as follows:

(a) REFLNS [Scheme scheme80]

(b) REFLNS_SCALE [Scheme scheme81]

(c) REFLNS_SHELL [Scheme scheme82]

(d) REFLNS_CLASS [Scheme scheme83]

The bullet ([\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 ([\rightarrow]) 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 [\sim] symbol.

Data items in the REFLNS category of the core CIF dictionary can be used to summarize the properties or attributes of the complete set of reflections used in refinement (Section 3.2.3.2.2[link] ). The mmCIF dictionary adds a number of data items to this category, including the formal category key required by the DDL2 data model. There are also data items for describing the data-reduction method and recording any relevant details about data reduction, and for giving an estimate of the overall Wilson B factor for the data set.

A number of the new data items relate to the issue of how reflections are flagged as being observed and are thus used in the refinement. In the core CIF dictionary, the criteria used to consider a reflection as being observed are given using the data item _reflns.observed_criterion. This is a free-text field so is not automatically parsable. Therefore it is supplemented in the mmCIF dictionary by data items that can be used to stipulate the criterion in terms of the values of F, I or the uncertainties in these quantities (Example 3.6.6.13[link]). The percentage of the total number of reflections that meet the criterion can be recorded.

Example 3.6.6.13. The data set used in the refinement of an HIV-1 protease structure (PDB 5HVP) described using data items in the REFLNS and REFLNS_SHELL categories.

[Scheme scheme84]

Data items are also provided for describing the selection of the reflections used to calculate the free R factor, and for giving the Rmerge values for all reflections and for the subset of `observed' reflections. Data items in the REFLNS_SCALE and REFLNS_SHELL categories are used in the same way in the mmCIF and core CIF dictionaries, and Section 3.2.3.2.2[link] can be consulted for details.

As with the related categories DIFFRN_REFLNS_CLASS and REFINE_LS_CLASS, the core dictionary category REFLNS_CLASS was introduced after the release of the first version of the mmCIF dictionary. It provides a more general way of describing the treatment of particular subsets of the observations, but it is not expected to be used in macromolecular structural studies, where partition by shells of resolution is traditional.








































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