Factors influencing estimates of coordinate error for molecular replacement.
Acta crystallographica. Section D, Structural biology
Blackwell Publishing Inc.
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Hatti, K., McCoy, A., Oeffner, R., Sammito, M., & Read, R. (2020). Factors influencing estimates of coordinate error for molecular replacement.. Acta crystallographica. Section D, Structural biology, 76 (Pt 1), 19-27. https://doi.org/10.1107/s2059798319015730
Good prior estimates of the effective root-mean-square deviation (RMSD) between atomic coordinates of the model and the target optimise the signal in molecular replacement, thereby increasing the success rate in difficult cases. Previous studies using protein structures solved by X-ray crystallography as models showed that optimal error estimates (refined after structure solution) were correlated with sequence identity between the model and target, and with the number of residues in the model. Here we have extended this work to find additional correlations between parameters of the model and target and hence improved prior estimates of the coordinate error. Using a graph database, a curated set of 6,030 molecular replacement calculations using models that had been solved by X-ray crystallography was analysed to consider about 120 model and target parameters. Improved estimates were achieved by replacing the sequence identity with the Gonnet score for sequence similarity, as well as by considering the resolution of the target structure and the MolProbity score of the model. This approach was extended by analysing 12,610 additional molecular replacement calculations where the model was determined by NMR. The median RMSD between pairs of models in an ensemble was found to be correlated with the estimated RMSD to the target. For models solved by NMR, the overall coordinate error estimates were larger than for structures determined by X-ray crystallography, and were more highly correlated with the number of residues.
Proteins, Crystallography, X-Ray, Magnetic Resonance Spectroscopy, Protein Conformation, Models, Molecular
National Institutes of Health (NIH) (via University of California) (6801943)
European Commission Horizon 2020 (H2020) Marie Sklodowska-Curie actions (790122)
Wellcome Trust (209407/Z/17/Z)
Wellcome Trust (082961/Z/07/A)
National Institute of General Medical Sciences (P01GM063210)
External DOI: https://doi.org/10.1107/s2059798319015730
This record's URL: https://www.repository.cam.ac.uk/handle/1810/299196
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