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Correcting pervasive errors in RNA crystallography through enumerative structure prediction

Abstract

Three-dimensional RNA models fitted into crystallographic density maps exhibit pervasive conformational ambiguities, geometric errors and steric clashes. To address these problems, we present enumerative real-space refinement assisted by electron density under Rosetta (ERRASER), coupled to Python-based hierarchical environment for integrated 'xtallography' (PHENIX) diffraction-based refinement. On 24 data sets, ERRASER automatically corrects the majority of MolProbity-assessed errors, improves the average Rfree factor, resolves functionally important discrepancies in noncanonical structure and refines low-resolution models to better match higher-resolution models.

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Figure 1: Examples of geometric improvements by ERRASER-PHENIX.
Figure 2: Improvements of the crystallographic models by ERRASER-PHENIX across the test cases.

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Acknowledgements

We thank J.S. Richardson for suggesting this problem and for detailed evaluation of the results we used to improve the program; C.L. Zirbel and N.B. Leontis for suggestions on base pair validation; B. Stoner and D. Herschlag for discussions on group I ribozyme active site; T. Terwilliger and J. Headd for aid in integrating ERRASER into PHENIX; S. Lyskov for setting up the ERRASER protocol on the ROSIE Server; members of the Das lab for comments on the manuscript; and members of the Rosetta and the PHENIX communities for discussions and code sharing. Computations were performed on the BioX2 cluster (US National Science Foundation CNS-0619926) and the Extreme Science and Engineering Discovery Environment resources (US National Science Foundation OCI-1053575). This work was supported by funding from US National Institutes of Health (R21 GM102716 to R.D. and R01 AI72012 to T.H.), a Burroughs-Wellcome Career Award at Scientific Interface (R.D.), Governmental Scholarship for Study Abroad of Taiwan and Howard Hughes Medical Institute International Student Research Fellowship (F.-C.C.), and the C.V. Starr Asia/Pacific Stanford Graduate Fellowship (P.S.).

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Contributions

F.-C.C., P.S. and R.D. designed the research. F.-C.C. implemented the methods and analyzed the results. P.S. provided code and assisted in data analysis. S.M.D. and T.H. provided the starting model and diffraction data of the unreleased 3TZR structure and evaluated its refinement. F.-C.C. and R.D. prepared the manuscript. All authors reviewed the manuscript.

Corresponding author

Correspondence to Rhiju Das.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–2, Supplementary Tables 1–13, Supplementary Results, Supplementary Notes (PDF 932 kb)

Supplementary Data

The ERRASER/PHENIX remodeled structures (PDB files). (ZIP 5752 kb)

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Chou, FC., Sripakdeevong, P., Dibrov, S. et al. Correcting pervasive errors in RNA crystallography through enumerative structure prediction. Nat Methods 10, 74–76 (2013). https://doi.org/10.1038/nmeth.2262

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