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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. 19.1, p. 421
Section 19.1.6. Refinement
aDepartment of Biochemistry and Molecular Biology, CLSC 161A, University of Chicago, Chicago, IL 60637, USA |
The methodologies employed to refine neutron data are essentially the same as those used in most X-ray studies. These include real-space (Hanson & Schoenborn, 1981![[link]](/graphics/greenarr.gif)
; Norvell & Schoenborn, 1976; Schoenborn & Diamond, 1976), reciprocal-space (Bentley & Mason, 1980; Phillips, 1984; Wlodawer & Hendrickson, 1982; Wlodawer & Sjolin, 1981) and restrained difference-map refinement (Kossiakoff & Spencer, 1980; 1981). A joint refinement technique in which the neutron and X-ray data are refined simultaneously has been developed (Wlodawer & Hendrickson, 1982). In addition to the normal difficulties encountered in the refinement of any protein structure, there are several that are peculiar to the neutron-diffraction technique. These special problems arise from the close proximity of hydrogen atoms to their parent atoms, coupled with the effects of the negative scattering length of the hydrogen atoms. Potential problems exist when the difference density generated from positional errors of one atom overlaps an adjacent atom site. The situation is further complicated by the fact that, because of its negative scattering length, an error in a hydrogen-atom position is minimized by moving the atom down the gradient, that is, in the opposite direction to that required for correcting parent-atom positions. To evaluate the extent of this problem in refinement, a test was devised using a 2.2 Å data set (Kossiakoff & Spencer, 1981). The coordinates of the protein trypsin were perturbed by a varying, but known, amount from their ideal positions. It was determined that, in general, convergence towards the true coordinate could be obtained when the coordinate errors were less than 0.3 Å; however, if the parent atom (an atom with one or more hydrogens attached to it) was displaced by more than 0.6 Å from its correct position, the effect of neighbouring hydrogens rendered the calculated shifts inaccurate. The results of this study support the observations of other investigators that it is absolutely crucial that the starting phasing model be of high quality, because the range of convergence of a neutron analysis is relatively small.
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