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

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Abstract

In 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. The ResProx web server is available at http://www.resprox.ca.

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Acknowledgments

Funding for this project was provided by the Alberta Prion Research Institute (APRI), PrioNet, and the Natural Sciences and Engineering Research Council (NSERC).

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Authors and Affiliations

  1. Department of Computing Science, University of Alberta, Edmonton, AB, Canada

    Mark Berjanskii, Jianjun Zhou, Yongjie Liang, Guohui Lin & David S. Wishart

  2. Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada

    David S. Wishart

  3. National Research Council, National Institute for Nanotechnology (NINT), Edmonton, AB, T6G 2E8, Canada

    David S. Wishart

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  1. Mark Berjanskii
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  2. Jianjun Zhou
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  3. Yongjie Liang
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  4. Guohui Lin
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  5. David S. Wishart
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Correspondence to David S. Wishart.

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Berjanskii, M., Zhou, J., Liang, Y. et al. Resolution-by-proxy: a simple measure for assessing and comparing the overall quality of NMR protein structures. J Biomol NMR 53, 167–180 (2012). https://doi.org/10.1007/s10858-012-9637-2

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  • DOI: https://doi.org/10.1007/s10858-012-9637-2

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