Literature DB >> 22628654

Linking crystallographic model and data quality.

P Andrew Karplus1, Kay Diederichs.   

Abstract

In macromolecular x-ray crystallography, refinement R values measure the agreement between observed and calculated data. Analogously, R(merge) values reporting on the agreement between multiple measurements of a given reflection are used to assess data quality. Here, we show that despite their widespread use, R(merge) values are poorly suited for determining the high-resolution limit and that current standard protocols discard much useful data. We introduce a statistic that estimates the correlation of an observed data set with the underlying (not measurable) true signal; this quantity, CC*, provides a single statistically valid guide for deciding which data are useful. CC* also can be used to assess model and data quality on the same scale, and this reveals when data quality is limiting model improvement.

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Year:  2012        PMID: 22628654      PMCID: PMC3457925          DOI: 10.1126/science.1218231

Source DB:  PubMed          Journal:  Science        ISSN: 0036-8075            Impact factor:   47.728


  13 in total

Review 1.  Remarks about protein structure precision.

Authors:  D W Cruickshank
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  1999-03

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3.  Substructure solution with SHELXD.

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4.  Free R value: a novel statistical quantity for assessing the accuracy of crystal structures.

Authors:  A T Brünger
Journal:  Nature       Date:  1992-01-30       Impact factor: 49.962

5.  Improved R-factors for diffraction data analysis in macromolecular crystallography.

Authors:  K Diederichs; P A Karplus
Journal:  Nat Struct Biol       Date:  1997-04

6.  A computer-linked cathode-ray tube microdensitometer for x-ray crystallography.

Authors:  U W Arndt; R A Crowther; J F Mallett
Journal:  J Sci Instrum       Date:  1968-05

7.  Crystal structure of mammalian cysteine dioxygenase. A novel mononuclear iron center for cysteine thiol oxidation.

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Journal:  J Biol Chem       Date:  2006-04-11       Impact factor: 5.157

Review 8.  Scaling and assessment of data quality.

Authors:  Philip Evans
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2005-12-14

9.  An introduction to data reduction: space-group determination, scaling and intensity statistics.

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10.  Fisher's information in maximum-likelihood macromolecular crystallographic refinement.

Authors:  Roberto A Steiner; Andrey A Lebedev; Garib N Murshudov
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2003-11-27
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