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. 21.1, p. 499   | 1 | 2 |

Section 21.1.3.3. Global statistics

G. J. Kleywegta*

aDepartment of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, SE-751 24 Uppsala, Sweden
Correspondence e-mail: gerard@xray.bmc.uu.se

21.1.3.3. Global statistics

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The crystallographic R value used to be the major global quality indicator until it was realised that it can easily be fooled, especially at low resolution (Brändén & Jones, 1990[link]; Jones et al., 1991[link]; Brünger, 1992a[link]; Kleywegt & Jones, 1995b[link]). The free R value, introduced by Brünger (1992a[link], 1993[link]), has been shown to be much more reliable and harder to manipulate (Kleywegt & Brünger, 1996[link]; Brünger, 1997[link]). It is excellently suited for monitoring the progress of refinement, for detecting major problems with model or data and for helping reduce over-fitting of the data (which occurs if many more parameters are refined in a model than is warranted by the information content of the crystallographic data). Moreover, the free R value can be used to estimate the coordinate error of the final model (Kleywegt et al., 1994[link]; Kleywegt & Brünger, 1996[link]; Brünger, 1997[link]; Cruickshank, 1999[link]).

In addition, the average or r.m.s. values for many of the local statistics, their minimum or maximum values or the percentage of outliers can be quoted and used to obtain an impression of the overall quality of the model and the overall fit of the model to the data.

References

First citationBrändén, C.-I. & Jones, T. A. (1990). Between objectivity and subjectivity. Nature (London), 343, 687–689.Google Scholar
First citationBrünger, A. T. (1992a). Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature (London), 355, 472–475.Google Scholar
First citationBrünger, A. T. (1993). Assessment of phase accuracy by cross validation: the free R value. Methods and applications. Acta Cryst. D49, 24–36.Google Scholar
First citationBrünger, A. T. (1997). The free R value: a more objective statistic for crystallography. Methods Enzymol. 277, 366–396.Google Scholar
First citation Cruickshank, D. W. J. (1999). Remarks about protein structure precision. Acta Cryst. D55, 583–601.Google Scholar
First citation Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Cryst. A47, 110–119.Google Scholar
First citation Kleywegt, G. J., Bergfors, T., Senn, H., Le Motte, P., Gsell, B., Shudo, K. & Jones, T. A. (1994). Crystal structures of cellular retinoic acid binding proteins I and II in complex with all-trans-retinoic acid and a synthetic retinoid. Structure, 2, 1241–1258.Google Scholar
First citation Kleywegt, G. J. & Brünger, A. T. (1996). Checking your imagination: applications of the free R value. Structure, 4, 897–904.Google Scholar
First citation Kleywegt, G. J. & Jones, T. A. (1995b). Where freedom is given, liberties are taken. Structure, 3, 535–540.Google Scholar








































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