Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Brief Communication
  • Published:

Correcting pervasive errors in RNA crystallography through enumerative structure prediction

Nature Methods volume 10, pages 74–76 (2013)Cite this article

Subjects

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.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

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

Similar content being viewed by others

Accession codes

Accessions

Protein Data Bank

References

  1. Ban, N., Nissen, P., Hansen, J., Moore, P.B. & Steitz, T.A. Science 289, 905–920 (2000).

    Article  CAS  Google Scholar 

  2. Gesteland, R.F., Cech, T. & Atkins, J.F. (eds.). The RNA World: The Nature of Modern RNA Suggests a Prebiotic RNA World. 3rd edn. (Cold Spring Harbor Laboratory Press, 2006).

  3. Keating, K.S. & Pyle, A.M. Proc. Natl. Acad. Sci. USA 107, 8177–8182 (2010).

    Article  CAS  Google Scholar 

  4. Read, R.J. et al. Structure 19, 1395–1412 (2011).

    Article  CAS  Google Scholar 

  5. Wang, X. et al. J. Math. Biol. 56, 253–278 (2008).

    Article  Google Scholar 

  6. Das, R. & Baker, D. Proc. Natl. Acad. Sci. USA 104, 14664–14669 (2007).

    Article  CAS  Google Scholar 

  7. Das, R., Karanicolas, J. & Baker, D. Nat. Methods 7, 291–294 (2010).

    Article  CAS  Google Scholar 

  8. Sripakdeevong, P., Kladwang, W. & Das, R. Proc. Natl. Acad. Sci. USA 108, 20573–20578 (2011).

    Article  CAS  Google Scholar 

  9. DiMaio, F., Tyka, M.D., Baker, M.L., Chiu, W. & Baker, D. J. Mol. Biol. 392, 181–190 (2009).

    Article  CAS  Google Scholar 

  10. DiMaio, F. et al. Nature 473, 540–543 (2011).

    Article  CAS  Google Scholar 

  11. Chen, V.B. et al. Acta Crystallogr. D Biol. Crystallogr. 66, 12–21 (2010).

    Article  CAS  Google Scholar 

  12. Richardson, J.S. et al. RNA 14, 465–481 (2008).

    Article  CAS  Google Scholar 

  13. Cruz, J.A. et al. RNA 18, 610–625 (2012).

    Article  CAS  Google Scholar 

  14. Forconi, M. et al. Angew. Chem. Int. Edn. 48, 7171–7175 (2009).

    Article  CAS  Google Scholar 

  15. Gendron, P., Lemieux, S. & Major, F. J. Mol. Biol. 308, 919–936 (2001).

    Article  CAS  Google Scholar 

  16. Brunger, A.T. Nature 355, 472–475 (1992).

    Article  CAS  Google Scholar 

  17. Dibrov, S.M. et al. Proc. Natl. Acad. Sci. USA 109, 5223–5228 (2012).

    Article  CAS  Google Scholar 

  18. Mandell, D.J., Coutsias, E.A. & Kortemme, T. Nat. Methods 6, 551–552 (2009).

    Article  CAS  Google Scholar 

  19. Adams, P.D. et al. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010).

    Article  CAS  Google Scholar 

  20. Winn, M.D., Isupov, M.N. & Murshudov, G.N. Acta Crystallogr. D Biol. Crystallogr. 57, 122–133 (2001).

    Article  CAS  Google Scholar 

  21. Headd, J.J. et al. Acta Crystallogr. D Biol. Crystallogr. 68, 381–390 (2012).

    Article  CAS  Google Scholar 

  22. Praznikar, J., Afonine, P.V., Guncar, G., Adams, P.D. & Turk, D. Acta Crystallogr. D Biol. Crystallogr. 65, 921–931 (2009).

    Article  CAS  Google Scholar 

  23. Afonine, P.V. et al. J. Appl. Cryst. 43, 669–676 (2010).

    Article  CAS  Google Scholar 

  24. Chen, V.B., Davis, I.W. & Richardson, D.C. Protein Sci. 18, 2403–2409 (2009).

    Article  CAS  Google Scholar 

Download references

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.).

Author information

Authors and Affiliations

  1. Department of Biochemistry, Stanford University, Stanford, California, USA

    Fang-Chieh Chou & Rhiju Das

  2. Biophysics Program, Stanford University, Stanford, California, USA

    Parin Sripakdeevong & Rhiju Das

  3. Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California, USA

    Sergey M Dibrov & Thomas Hermann

  4. Department of Physics, Stanford University, Stanford, California, USA

    Rhiju Das

Authors
  1. Fang-Chieh Chou
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Parin Sripakdeevong
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Sergey M Dibrov
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Thomas Hermann
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Rhiju Das
    View author publications

    You can also search for this author in PubMed Google Scholar

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.

Ethics declarations

Competing interests

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)

Rights and permissions

Reprints and permissions

About this article

Cite this article

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

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nmeth.2262

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing