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. 154-155

Section 3.6.6.1.4. Phasing via multiple-wavelength anomalous dispersion

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

3.6.6.1.4. Phasing via multiple-wavelength anomalous dispersion

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The data items in these categories are as follows:

(a) PHASING_MAD [Scheme scheme44]

(b) PHASING_MAD_CLUST [Scheme scheme45]

(c) PHASING_MAD_EXPT [Scheme scheme46]

(d) PHASING_MAD_RATIO [Scheme scheme47]

(e) PHASING_MAD_SET [Scheme scheme48]

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.

PHASING_MAD and related categories are used to provide information about phasing using the multiple-wavelength anomalous dispersion (MAD) technique. The data model used for MAD phasing in the current version of the mmCIF dictionary is that of Hendrickson, as exemplified in the structure determination of N-cadherin (Shapiro et al., 1995[link]; Example 3.6.6.4[link]). In current practice, MAD phasing is often treated as a special case of MIR phasing and the PHASING_MIR categories would be more appropriate to describe the results.

Example 3.6.6.4. MAD phasing of the structure of N-cadherin (Shapiro et al., 1995[link]) described using data items in the PHASING_MAD and related categories.

[Scheme scheme49]

Unlike the PHASING_MIR categories, there is no provision in the current mmCIF model of MAD phasing for analysis of the overall phasing statistics and the contribution to the phasing of each data set by bins of resolution, and no provision for giving a list of the phased reflections. This will need to be addressed in future versions of the mmCIF dictionary.

The relationships between categories describing MAD phasing are shown in Fig. 3.6.6.1[link].

[Figure 3.6.6.1]

Figure 3.6.6.1 | top | pdf |

The family of categories used to describe MAD phasing. Boxes surround categories of related data items. Data items that serve as category keys are preceded by a bullet ([\bullet]). Lines show relationships between linked data items in different categories with arrows pointing at the parent data items.

Data items in the PHASING_MAD category allow a brief overview of the method that was used to be given and allow special aspects of the phasing strategy to be noted; data items in this category are analogous to the data items in the other overview categories describing phasing techniques.

In the data model for MAD phasing used in the present version of the mmCIF dictionary, a collection of data sets measured at different wavelengths can be used to construct more than one set of phases. These phase sets will produce electron-density maps with different local properties. The model of the structure is often constructed using information from a collection of these maps. The collections of multiple phase sets are referred to as `experiments' and the groups of data sets that contribute to each experiment are referred to as `clusters'. Data items in PHASING_MAD_EXPT identify each experiment and give the number of contributing clusters. Additional data items record the phase difference between the structure factors due to normal scattering from all atoms and from only the anomalous scatterers, the standard uncertainty of this quantity, the mean figure of merit, and a number of other indicators of the quality of the phasing.

Data items in the PHASING_MAD_CLUST category can be used to label the clusters of data sets and give the number of data sets allocated to each cluster. In Example 3.6.6.4[link] two experiments are described. The first experiment contains two clusters, one of which contains four data sets and the second of which contains five data sets. The second experiment contains a single cluster of five data sets. Note that the author has chosen informative labels to identify the clusters (`four wavelength', `five wavelength'). Carefully chosen labels can help someone reading the mmCIF to trace the complex relationships between the categories.

Data items in the PHASING_MAD_RATIO category can be used to record the ratios of phasing statistics (Bijvoet differences) between pairs of data sets in a MAD phasing experiment, within shells of resolution characterized by _phasing_MAD_ratio.d_res_high and *.d_res_low.

The data sets used in the MAD phasing experiments are described using data items in the PHASING_MAD_SET category. Each data set is characterized by resolution shell and wavelength, and by the [f'] and [f''] components of the anomalous scattering factor at that wavelength. The actual observations in each data set and the experimental conditions under which they were made are recorded using data items in the PHASING_SET and PHASING_SET_REFLN categories.

References

Shapiro, L., Fannon, A. M., Kwong, P. D., Thompson, A., Lehmann, M. S., Grubel, G., Legrand, J. F., Als-Nielsen, J., Colman, D. R. & Hendrickson, W. A. (1995). Structural basis of cell–cell adhesion by cadherins. Nature (London), 374, 327–337.








































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