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. 25.2, p. 737   | 1 | 2 |

Section 25.2.10.4.6. Modelling disorder and solvent

G. M. Sheldricku*

25.2.10.4.6. Modelling disorder and solvent

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There are many ways of modelling disorder using SHELXL, but for macromolecules the most convenient is to retain the same atom and residue names for the two or more components and assign a different `part number' (analogous to the PDB alternative site flag) to each component. With this technique, no change is required to the input restraints etc. Atoms in the same component will normally have a common occupancy that is assigned to a `free variable'. If there are only two components, the sum of their occupancies can be constrained to be unity; if there are more than two components, the sum of their free variables may be restrained to be unity. Since any linear restraint may be applied to the free variables, they are very flexible, e.g. for modelling complicated disorder. By restraining distances to be equal to a free variable, a standard deviation of the mean distance may be calculated rigorously using full-matrix least-squares algebra.

Babinet's principle is used to define a bulk solvent model with two refinable parameters (Moews & Kretsinger, 1975[link]), and global anisotropic scaling (Usón et al., 1999[link]) may be applied using a parameterization proposed by Parkin et al. (1995)[link]. An auxiliary program, SHELXWAT, allows automatic water divining by iterative least-squares refinement, rejection of waters with high displacement parameters, difference-electron-density calculation, and a peak search for potential water molecules that make at least one good hydrogen bond and no bad contacts; this is a simplified version of the ARP procedure of Lamzin & Wilson (1993)[link].

References

Lamzin, V. S. & Wilson, K. S. (1993). Automated refinement of protein models. Acta Cryst. D49, 129–147.Google Scholar
Moews, P. C. & Kretsinger, R. H. (1975). Refinement of carp muscle parvalbumin by model building and difference Fourier analysis. J. Mol. Biol. 91, 201–228.Google Scholar
Parkin, S., Moezzi, B. & Hope, H. (1995). XABS2: an empirical absorption correction program. J. Appl. Cryst. 28, 53–56.Google Scholar
Usón, I., Pohl, E., Schneider, T. R., Dauter, Z., Schmidt, A., Fritz, H.-J. & Sheldrick, G. M. (1999). 1.7 Å structure of the stabilised RE!v mutant T39K. Application of local NCS restraints. Acta Cryst. D55, 1158–1167.Google Scholar








































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