International
Tables for
Crystallography
Volume F
Crystallography of biological macromolecules
Edited by M. G. Rossmann and E. Arnold

International Tables for Crystallography (2006). Vol. F, ch. 16.1, pp. 337-338   | 1 | 2 |

Section 16.1.7.2. Parameters and procedures

G. M. Sheldrick,c H. A. Hauptman,b C. M. Weeks,b* R. Millerb and I. Usóna

aInstitut für Anorganisch Chemie, Universität Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany,bHauptman–Woodward Medical Research Institute, Inc., 73 High Street, Buffalo, NY 14203-1196, USA, and cLehrstuhl für Strukturchemie, Universität Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany
Correspondence e-mail:  weeks@orion.hwi.buffalo.edu

16.1.7.2. Parameters and procedures

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All of the major parameters of the Shake-and-Bake 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 [N_{u}], the number of unique non-H atoms in the asymmetric unit. These parameters have been fine-tuned in a series of tests using data for both small and large molecules (Weeks, DeTitta et al., 1994[link]; Chang et al., 1997[link]; Weeks & Miller, 1999b[link]). Default (recommended) parameter values used in the SnB program are summarized in Table 16.1.7.1[link]. 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 dual-space 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 peak-wavelength anomalous-difference data for S-adenosylhomocysteine (AdoHcy) hydrolase (Turner et al., 1998[link]). Parameter shift with a maximum of two 90° steps [indicated by the shorthand notation PS(90°, 2)] is the default phase-refinement 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[link]). This seems to reduce the frequency of false minima (see Section 16.1.8.2[link]).

Table 16.1.7.1| top | pdf |
Recommended parameter values for the SnB program

Values are expressed in terms of Nu, the number of unique non-H atoms (solvent atoms are typically ignored). Full-structure recommendations are for data sets measured to 1.1 Å resolution or better. Only heavy atoms or anomalous scatterers are counted for substructures.

ParameterFull structuresSubstructures
Phases 10Nu 30Nu
Triplet invariants 100Nu 300Nu
Peaks (with S, Cl) 0.4Nu Nu
Peaks (no `heavy') 0.8Nu  
Cycles Nu/2 if [N_{u} \lt 100] or if [N_{u} \lt 400] with S, Cl etc.; Nu otherwise 2Nu (minimum 20)

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[link] for details).

References

Chang, C.-S., Weeks, C. M., Miller, R. & Hauptman, H. A. (1997). Incorporating tangent refinement in the Shake-and-Bake formalism. Acta Cryst. A53, 436–444.Google Scholar
Deacon, A. M., Weeks, C. M., Miller, R. & Ealick, S. E. (1998). The Shake-and-Bake structure determination of triclinic lysozyme. Proc. Natl Acad. Sci. USA, 95, 9284–9289.Google Scholar
Turner, M. A., Yuan, C.-S., Borchardt, R. T., Hershfield, M. S., Smith, G. D. & Howell, P. L. (1998). Structure determination of selenomethionyl S-adenosylhomocysteine hydrolase using data at a single wavelength. Nature Struct. Biol. 5, 369–375.Google Scholar
Weeks, C. M., DeTitta, G. T., Hauptman, H. A., Thuman, P. & Miller, R. (1994). Structure solution by minimal-function phase refinement and Fourier filtering. II. Implementation and applications. Acta Cryst. A50, 210–220.Google Scholar
Weeks, C. M. & Miller, R. (1999b). Optimizing Shake-and-Bake for proteins. Acta Cryst. D55, 492–500.Google Scholar








































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