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Version 1.2 of the Crystallography and NMR system - Nature Protocols

  • ️Brunger, Axel T
  • ️Thu Oct 25 2007
  • Protocol
  • Published: 25 October 2007

Nature Protocols volume 2, pages 2728–2733 (2007)Cite this article

Abstract

Version 1.2 of the software system, termed Crystallography and NMR system (CNS), for crystallographic and NMR structure determination has been released. Since its first release, the goals of CNS have been (i) to create a flexible computational framework for exploration of new approaches to structure determination, (ii) to provide tools for structure solution of difficult or large structures, (iii) to develop models for analyzing structural and dynamical properties of macromolecules and (iv) to integrate all sources of information into all stages of the structure determination process. Version 1.2 includes an improved model for the treatment of disordered solvent for crystallographic refinement that employs a combined grid search and least-squares optimization of the bulk solvent model parameters. The method is more robust than previous implementations, especially at lower resolution, generally resulting in lower R values. Other advances include the ability to apply thermal factor sharpening to electron density maps. Consistent with the modular design of CNS, these additions and changes were implemented in the high-level computing language of CNS.

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References

  1. Brunger, A.T. et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. 54 (Part 5): 905–921 (1998).

    CAS  Google Scholar 

  2. Brunger, A.T. X-PLOR, version 3.1. A System for X-ray Crystallography and NMR (Yale University Press, New Haven, Connecticut, USA, 1992).

    Google Scholar 

  3. Schwieters, C.D., Kuszewski, J.J., Tjandra, N. & Clore, G.M. The Xplor-NIH NMR molecular structure determination package. J. Magn. Reson. 160, 65–73 (2003).

    Article  CAS  Google Scholar 

  4. Dominguez, C., Boelens, R. & Bonvin, A.M. HADDOCK: a protein–protein docking approach based on biochemical or biophysical information. J. Am. Chem. Soc. 125, 1731–1737 (2003).

    Article  CAS  Google Scholar 

  5. Linge, J.P., Habeck, M., Rieping, W. & Nilges, M. ARIA: automated NOE assignment and NMR structure calculation. Bioinformatics (Oxford, England) 19, 315–316 (2003).

    Article  CAS  Google Scholar 

  6. Moulinier, L., Case, D.A. & Simonson, T. Reintroducing electrostatics into protein X-ray structure refinement: bulk solvent treated as a dielectric continuum. Acta Crystallogr. 59, 2094–2103 (2003).

    Google Scholar 

  7. Wall, M.E., Subramaniam, S. & Phillips, G.N. Jr. Protein structure determination using a database of interatomic distance probabilities. Protein Sci. 8, 2720–2727 (1999).

    Article  CAS  Google Scholar 

  8. Clarage, J.B. & Phillips, G.N. Jr. Cross-validation tests of time-averaged molecular dynamics refinements for determination of protein structures by X-ray crystallography. Acta Crystallogr. 50, 24–36 (1994).

    CAS  Google Scholar 

  9. Wang, H. & Stubbs, G. Molecular dynamics in refinement against fiber diffraction data. Acta Crystallogr. A 49, 504–513 (1993).

    Article  CAS  Google Scholar 

  10. Grosse-Kunstleve, R. & Adams, P. On the handling of atomic anisotropic displacement parameters. J. Appl. Crystallogr. 35, 477–480 (2002).

    Article  CAS  Google Scholar 

  11. Lee, B. & Richards, F.M. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55, 379–400 (1971).

    Article  CAS  Google Scholar 

  12. Richards, F.M. Calculation of molecular volumes and areas for structures of known geometry. Methods Enzymol. 115, 440–464 (1985).

    Article  CAS  Google Scholar 

  13. Phillips, S.E. Structure and refinement of oxymyoglobin at 1.6 Å resolution. J. Mol. Biol. 142, 531–554 (1980).

    Article  CAS  Google Scholar 

  14. Afonine, P.V., Grosse-Kunstleve, R.W. & Adams, P.D. A robust bulk-solvent correction and anisotropic scaling procedure. Acta Crystallogr. 61, 850–855 (2005).

    Article  Google Scholar 

  15. Jiang, J.S. & Brunger, A.T. Protein hydration observed by X-ray diffraction. Solvation properties of penicillopepsin and neuraminidase crystal structures. J. Mol. Biol. 243, 100–115 (1994).

    Article  CAS  Google Scholar 

  16. DeLaBarre, B. & Brunger, A.T. Complete structure of p97/valosin-containing protein reveals communication between nucleotide domains. Nat. Struct. Biol. 10, 856–863 (2003).

    Article  CAS  Google Scholar 

  17. DeLaBarre, B. & Brunger, A.T. Nucleotide dependent motion and mechanism of action of p97/VCP. J. Mol. Biol. 347, 437–452 (2005).

    Article  CAS  Google Scholar 

  18. Bass, R.B., Strop, P., Barclay, M. & Rees, D.C. Crystal structure of Escherichia coli MscS, a voltage-modulated and mechanosensitive channel. Science 298, 1582–1587 (2002).

    Article  CAS  Google Scholar 

  19. DeLaBarre, B. & Brunger, A.T. Considerations for the refinement of low-resolution crystal structures. Acta Crystallogr. 62, 923–932 (2006).

    Google Scholar 

  20. Westbrook, J.D. & Fitzgerald, P.M. The PDB format, mmCIF, and other data formats. Methods Biochem. Anal. 44, 161–179 (2003).

    CAS  PubMed  Google Scholar 

  21. CCP. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. 50, 760–763 (1994).

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Acknowledgements

I am grateful to Paul Adams and Byron DeLaBarre for stimulating discussions.

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Authors and Affiliations

  1. The Howard Hughes Medical Institute and Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Structural Biology, and Photon Science, Stanford University, J.H. Clark Center E300C, 318 Campus Dr., California, 94305, USA

    Axel T Brunger

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  1. Axel T Brunger

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Correspondence to Axel T Brunger.

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Brunger, A. Version 1.2 of the Crystallography and NMR system. Nat Protoc 2, 2728–2733 (2007). https://doi.org/10.1038/nprot.2007.406

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  • Published: 25 October 2007

  • Issue Date: November 2007

  • DOI: https://doi.org/10.1038/nprot.2007.406