Resolution-by-proxy : a simple measure for assessing and comparing the overall quality of NMR protein structures

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DOIResolve DOI: http://doi.org/10.1007/s10858-012-9637-2
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TypeArticle
Journal titleJournal of Biomolecular NMR
ISSN0925-2738
1573-5001
Volume53
Issue3
Pages167180; # of pages: 14
Subjectprotein; structure; quality; NMR; x-ray resolution
AbstractIn protein X-ray crystallography, resolution is often used as a good indicator of structural quality. Diffraction resolution of protein crystals correlates well with the number of X-ray observables that are used in structure generation and, therefore, with protein coordinate errors. In protein NMR, there is no parameter identical to X-ray resolution. Instead, resolution is often used as a synonym of NMR model quality. Resolution of NMR structures is often deduced from ensemble precision, torsion angle normality and number of distance restraints per residue. The lack of common techniques to assess the resolution of X-ray and NMR structures complicates the comparison of structures solved by these two methods. This problem is sometimes approached by calculating “equivalent resolution” from structure quality metrics. However, existing protocols do not offer a comprehensive assessment of protein structure as they calculate equivalent resolution from a relatively small number (<5) of protein parameters. Here, we report a development of a protocol that calculates equivalent resolution from 25 measurable protein features. This new method offers better performance (correlation coefficient of 0.92, mean absolute error of 0.28 Å) than existing predictors of equivalent resolution. Because the method uses coordinate data as a proxy for X-ray diffraction data, we call this measure “Resolution-by-Proxy” or ResProx. We demonstrate that ResProx can be used to identify under-restrained, poorly refined or inaccurate NMR structures, and can discover structural defects that the other equivalent resolution methods cannot detect.
Publication date
LanguageEnglish
AffiliationSecurity and Disruptive Technologies; National Research Council Canada
Peer reviewedYes
Identifier9637
NPARC number21268389
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Record identifier9eb24cc5-5323-4ab6-8ddf-3942b852e5d0
Record created2013-07-09
Record modified2016-05-09
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