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Free R value: a novel statistical quantity for assessing the accuracy of crystal structures

Nature volume ?355 ,? pages 472?475 ( 1992 ) Cite this article

Abstract

THE determination of macromolecular structure by crystallography involves fitting atomic models to the observed diffraction data 1 . The traditional measure of the quality of this fit, and presumably the accuracy of the model, is the R value. Despite stereochemical restraints 2 , it is possible to overfit or 'misfit' the diffraction data: an incorrect model can be refined to fairly good R values as several recent examples have shown 3 . Here I propose a reliable and unbiased indicator of the accuracy of such models. By analogy with the cross-validation method 4,5 of testing statistical models I define a statistical quantity ( R free T ) that measures the agreement between observed and computed structure factor amplitudes for a 'test' set of reflections that is omitted in the modelling and refinement process. As examples show, there is a high correlation between R free T and the accuracy of the atomic model phases. This is useful because experimental phase information is usually inaccurate, incomplete or unavailable. I expect that R free T will provide a measure of the information content of recently proposed models of thermal motion and disorder 6?8 , time-averaging 9 and bulk solvent 10 .

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References

  1. Jensen, L. H. Meth. Enzym. 115 , 227?234 (1985).

    Article   CAS   Google Scholar  

  2. Hendrickson, W. A. Meth. Enzym. 115 , 252?270 (1985).

    Article   CAS   Google Scholar  

  3. Branden, C. I. & Jones, A. Nature 343 , 687?689 (1990).

    Article   ADS   Google Scholar  

  4. Mosteller, F. & Tukey, J. W. Data Analysis and Regression: a Second Course in Statistics (Addison-Wesley, Reading, Massachusetts, 1977).

    Google Scholar  

  5. Efron, B. & Tibshirani, R. Science 253 , 390?395 (1991).

    Article   ADS   CAS   Google Scholar  

  6. Diamond, R. Acta crystallogr. A46 , 425?435 (1990).

    Article   CAS   Google Scholar  

  7. Kuriyan, J. & Weis, W. I. Proc. natn. Acad. Sci. U.S.A. 88 , 2773?2777 (1991).

    Article   ADS   CAS   Google Scholar  

  8. Kuriyan, J. et al. Proteins 10 , 340?358 (1991).

    Article   CAS   Google Scholar  

  9. Gros, P., Gunsteren, W. F. & Hol, W. G. J. Science 249 , 1149?1152 (1990).

    Article   ADS   CAS   Google Scholar  

  10. Badger, J. & Caspar, D. L. D. Proc. natn. Acad. Sci. U.S.A. 88 , 622?626 (1991).

    Article   ADS   CAS   Google Scholar  

  11. Stout, G. H. & Jensen, L. H. in X-ray Structure Determination, a Practical Guide 2nd edn 343?378 (Wiley, New York, 1989).

    Google Scholar  

  12. Press, W. H., Flannery, B. P., Teukolosky, S. A. & Vetterling, W. T. in Numerical Recipes 498?504 (Cambridge University Press, 1986).

    Google Scholar  

  13. Hamilton, W. C. Acta crystallogr. 18 , 502?510 (1965).

    Article   CAS   Google Scholar  

  14. Hsu, I.-N., Delbare, L. T. J., James, M. N. G. & Hofmann, T. Nature 266 , 140?145 (1977).

    Article   ADS   CAS   Google Scholar  

  15. James, M. N. G. & Sielecki, A. R. J. molec. Biol. 163 , 299?361 (1983).

    Article   CAS   Google Scholar  

  16. Brunger, A. T., Kuriyan, J. & Karplus, M. Science 235 , 458?460 (1987).

    Article   ADS   Google Scholar  

  17. Curmi, P. A. M., Schreuder, H., Cascio, D., Sweet, R. M. & Eisenberg, D. J. biol. Chem. (in the press).

  18. Chapman, M. S. et al. Science 241 , 71?74 (1988).

    Article   ADS   CAS   Google Scholar  

  19. Brunger, A. T. A. Rev. Phys. Chem. 42 , 197?233 (1991).

    Article   ADS   Google Scholar  

  20. Jack, A. & Levitt, M. Acta crystallogr. A34 , 931?935 (1978).

    Article   ADS   CAS   Google Scholar  

  21. Brooks, B. R. et al. J. comp. Chem. 4 , 187?217 (1983).

    Article   CAS   Google Scholar  

  22. Konnert, J. H. & Hendrickson, W. A. Acta crystallogr. A36 , 344?349 (1980).

    Article   ADS   CAS   Google Scholar  

  23. Ernst, R. R., Bodenhausen, G. & Wokaun, A. Principles of Nuclear Magnetic Resonance in One and Two Dimensions (Clarendon, Oxford, 1987).

    Google Scholar  

  24. Wuthrich, K., NMR of Proteins and Nucleic Acids (Wiley, New York, 1986).

    Book   Google Scholar  

  25. Brunger, A. T. J. molec. Biol. 203 , 803?816 (1988).

    Article   Google Scholar  

  26. Brunger, A. T., Krukowski, A. & Erickson, J. Acta crystallogr. A46 , 585?593 (1900).

    Google Scholar  

  27. Brunger, A. T. X-PLOR, Version 2.1, Yale University (1990).

  28. Read, R. Acta crystallogr. A42 , 140?149 (1986).

    Article   CAS   Google Scholar  

  29. Clore, G. M. & Gronenborn, A. M. Science 252 , 1390?1399 (1991).

    Article   ADS   CAS   Google Scholar  

Download references

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  1. The Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, 06511, USA

    Axel T. Brunger

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Brunger, A. Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355 , 472?475 (1992). https://doi.org/10.1038/355472a0

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