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. 15.2, p. 328   | 1 | 2 |

Section 15.2.6. Estimation of overall coordinate error

R. J. Reada*

aDepartment of Haematology, University of Cambridge, Wellcome Trust Centre for Molecular Mechanisms in Disease, CIMR, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 2XY, England
Correspondence e-mail: rjr27@cam.ac.uk

15.2.6. Estimation of overall coordinate error

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In principle, since the distribution of observed and calculated amplitudes is determined largely by the coordinate errors of the model, one can determine whether a particular coordinate-error distribution is consistent with the amplitudes. Unfortunately, it turns out that the coordinate errors cannot be deduced unambiguously, because many distributions of coordinate errors are consistent with a particular distribution of amplitudes (Read, 1990)[link].

If the simplifying assumption is made that all the atoms are subject to a single error distribution, then the parameter D (and thus the related parameter [\sigma_{A}]) varies with resolution as the Fourier transform of the error distribution, as discussed above. Two related methods to estimate overall coordinate error are based on the even more specific assumption that the coordinate-error distribution is Gaussian: the Luzzati plot (Luzzati, 1952)[link] and the [\sigma_{A}] plot (Read, 1986)[link]. Unfortunately, the central assumption is not justified; atoms that scatter more strongly (heavier atoms or atoms with lower B factors) tend to have smaller coordinate errors than weakly scattering atoms. The proportion of the structure factor contributed by well ordered atoms increases at high resolution, so that the structure factors agree better at high resolution than if there were a single error distribution.

It is often stated, optimistically, that the Luzzati plot provides an upper bound to the coordinate error, because the observation errors in [|{\bf F}_{O}|] have been ignored. This is misleading, because there are other effects that cause the Luzzati and [\sigma_{A}] plots to give underestimates (Read, 1990)[link]. Chief among these are the correlation of errors and scattering power and the overfitting of the amplitudes in structure refinement (discussed below). These estimates of overall coordinate error should not be interpreted too literally; at best, they provide a comparative measure.

References

Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802–810.Google Scholar
Read, R. J. (1986). Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Cryst. A42, 140–149.Google Scholar
Read, R. J. (1990). Structure-factor probabilities for related structures. Acta Cryst. A46, 900–912.Google Scholar








































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