International
Tables for Crystallography Volume F Crystallography of biological macromolecules Edited by M. G. Rossmann and E. Arnold © International Union of Crystallography 2006 
International Tables for Crystallography (2006). Vol. F, ch. 16.1, pp. 337338
Section 16.1.7.2. Parameters and procedures^{a}Institut für Anorganisch Chemie, Universität Göttingen, Tammannstrasse 4, D37077 Göttingen, Germany,^{b}Hauptman–Woodward Medical Research Institute, Inc., 73 High Street, Buffalo, NY 142031196, USA, and ^{c}Lehrstuhl für Strukturchemie, Universität Göttingen, Tammannstrasse 4, D37077 Göttingen, Germany 
All of the major parameters of the ShakeandBake procedure (i.e., the numbers of refinement cycles, phases, triplet invariant relationships and peaks selected) are a function of structure size and can be expressed in terms of , the number of unique nonH atoms in the asymmetric unit. These parameters have been finetuned in a series of tests using data for both small and large molecules (Weeks, DeTitta et al., 1994; Chang et al., 1997; Weeks & Miller, 1999b). Default (recommended) parameter values used in the SnB program are summarized in Table 16.1.7.1. At resolutions in the 1.1–1.4 Å range, recalcitrant data sets can sometimes be made to yield solutions if (1) the phase:invariant ratio is increased from 1:10 to values ranging between 1:20 and 1:50 or (2) the number of dualspace refinement cycles is doubled or tripled. The presence of moderately heavy atoms (e.g. S, C, Fe) greatly increases the probability of success at resolutions less than 1.2 Å; in general, the higher the fraction of such atoms the more the resolution requirement can be relaxed, provided that these atoms have low B values. Thus, disulfide bridges are much more helpful than methionine sulfur atoms because they tend to have lower B values. Parameter recommendations for substructures are based on an analysis of the peakwavelength anomalousdifference data for Sadenosylhomocysteine (AdoHcy) hydrolase (Turner et al., 1998). Parameter shift with a maximum of two 90° steps [indicated by the shorthand notation PS(90°, 2)] is the default phaserefinement mode. However, some structures (especially large P1 structures) may respond better to a single larger shift [e.g. PS(157.5°, 1)] (Deacon et al., 1998). This seems to reduce the frequency of false minima (see Section 16.1.8.2).

In general, the parameter values used in SHELXD are similar to those used in SnB. However, the combination of random omit maps with tangent extension has been found to be the most effective strategy within the context of SHELXD. Consequently, it is used as the default operational mode (see Section 16.1.8.4 for details).
References
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