Phasing data sets

Fitzgerald, P. M. D.; Westbrook, J. D.; Bourne, P. E.; McMahon, B.; Watenpaugh, K. D.; Berman, H. M.

doi:10.1107/97809553602060000738

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

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International Tables for Crystallography (2006). Vol. G. ch. 3.6, pp. 157-158

Section 3.6.6.1.6. Phasing data sets

P. M. D. Fitzgerald,^a ^* J. D. Westbrook,^b P. E. Bourne,^c B. McMahon,^d K. D. Watenpaugh^e and H. M. Berman^f

^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
Correspondence e-mail: paula_fitzgerald@merck.com

3.6.6.1.6. Phasing data sets

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The data items in these categories are as follows:

(a) PHASING_SET [Scheme scheme57]

(b) PHASING_SET_REFLN [Scheme scheme58]

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.

Data items in the PHASING_SET family of categories are homologous to items with related names in the CELL and DIFFRN families of categories. The PHASING_SET categories were added to the mmCIF data model so that intensity and phase information for the data sets used in phasing could be stored in the same data block as the information for the refined structure. It is not necessary to store all the experimental information for each data set (e.g. the raw data sets or crystal growth conditions); it is assumed that the full experimental description of each phasing set would be recorded in a separate data block (see Example 3.6.6.6).

Example 3.6.6.6. The phasing sets used in the structure determination of bovine plasma retinol-binding protein (Zanotti et al., 1993) described with data items in the PHASING_SET and PHASING_SET_REFLN categories.

[Scheme scheme59]

Data items in the PHASING_SET category identify each set of diffraction data used in a phasing experiment and can be used to summarize relevant experimental conditions. Because a given data set may be used in a number of different ways (for example, as an isomorphous derivative and as a component of a multiple-wavelength calculation), it is appropriate to store the reflections in a category distinct from either the PHASING_MAD or PHASING_MIR family of categories, but accessible to both these families (and any similar categories that might be introduced later to describe new phasing methods). Figs. 3.6.6.1 and 3.6.6.2 show how reference is made to the relevant sets from within the PHASING_MAD and PHASING_MIR categories.

Each phasing set is given a unique value of _phasing_set.id. The other PHASING_SET data items record the cell dimensions and angles associated with each phasing set, the wavelength of the radiation used in the experiment, the source of the radiation, the detector type, and the ambient temperature.

Data items in the PHASING_SET_REFLN category are used to record the values of the measured structure factors and their uncertainties. Several distinct data sets may be present in this list, with reflections in each set identified by the appropriate value of _phasing_set_refln.set_id.

References

Zanotti, G., Berni, R. & Monaco, H. L. (1993). Crystal structure of liganded and unliganded forms of bovine plasma retinol-binding protein. J. Biol. Chem. 268, 10728–10738.Google Scholar

International Tables for Crystallography (2006). Vol. G. ch. 3.6, pp. 157-158