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Automated Structure Solution With autoSHARP

  • Clemens Vonrhein
  • Eric Blanc
  • Pietro Roversi
  • Gérard Bricogne
Protocol
Part of the Methods in Molecular Biology™ book series (MIMB, volume 364)

Abstract

We present here the automated structure solution pipeline “autoSHARP.” It is built around the heavy-atom refinement and phasing program SHARP, the density modification program SOLOMON, and the ARP/wARP package for automated model building and refinement (using REFMAC). It allows fully automated structure solution, from merged reflection data to an initial model, without any user intervention. We describe and discuss the preparation of the user input, the data flow through the pipeline, and the various results obtained throughout the procedure.

Key Words

SHARP autoSHARP automation structure solution 

References

  1. 1.
    Bourne, S. R. (1978) Unix time-sharing system: The Unix shell. Bell Sys. Tech. J. 57, 1971–1990.Google Scholar
  2. 2.
    Wall, L., Christiansen, T., and Orwant, J. (2000) Programming Perl, 3rd ed., O’Reilly and Associates, Inc., Sebastopol, CA.Google Scholar
  3. 3.
    Collaborative Computational Project, Number 4 (1994) The CCP4 suite: programs for protein crystallography. Acta Cryst. D50, 760–763.Google Scholar
  4. 4.
    Otwinowski, Z. and Minor, W. (1997) Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, (Carter, C. W., Jr and Sweet, R. M., eds.), Academic Press, New York, NY, pp. 307–326.Google Scholar
  5. 5.
    Cromer, D. T. (1983) Calculation of anomalous scattering factors at arbitrary wavelengths. J. Appl. Cryst. 16, 437–438.CrossRefGoogle Scholar
  6. 6.
    Wilson, A. J. C. (1942) Determination of absolute from relative X-ray intensity. Nature 150, 151–152.Google Scholar
  7. 7.
    Matthews, B. W. (1968) The solvent content of protein crystals. J. Mol. Biol. 33, 491–497.PubMedCrossRefGoogle Scholar
  8. 8.
    Rossmann, M. G. and Blow, D. M. (1962) The detection of sub-units within the crystallographic asymmetric unit. Acta Cryst. 15, 24–31.CrossRefGoogle Scholar
  9. 9.
    Patterson, A. L. (1934) A Fourier series method for the determination of the components of interatomic distances in crystals. Phys. Rev. 46, 372–376.CrossRefGoogle Scholar
  10. 10.
    Eagles, P. A. M., Johnson, L. N., Joynson, M. A., McMurray, C. H., and Gutfreund, H. (1969) Subunit structure of aldolase: chemical and crystallographic evidence. J. Mol. Biol. 45, 533–544.PubMedCrossRefGoogle Scholar
  11. 11.
    Kraut, J., Sieker, L. C., High, D. F., and Freer, S. T. (1962) Chymotrypsinogen: a three-dimensional Fourier syntheis at 5AA resolution. Proc. Nat. Acad. Sci. USA 48, 1417–1424.PubMedCrossRefGoogle Scholar
  12. 12.
    Schneider, T. R. and Sheldrick, G. M. (2002) Substructure solution with SHELXD. Acta Cryst. D58, 1772–1779.Google Scholar
  13. 13.
    Weeks, C. M. and Miller, R. (1999) The design and implementation of SnB v2.0. J. Appl. Cryst. 32, 120–124.CrossRefGoogle Scholar
  14. 14.
    Grosse-Kunstleve, R. W. and Adams, P. D. (2003). Substructure search procedures for macromolecular structures. Acta Cryst. D59, 1966–1973.Google Scholar
  15. 15.
    Terwilliger, T. C. (2003) Automated structure solution, density modification and model building. Acta Cryst. D58, 1937–1940.Google Scholar
  16. 16.
    Ness, S. R., de Graaff, R. A. G., Abrahams, J. P., and Pannu, N. S. (2004). Crank: new methods for automated macromolecular crystal structure solution. Structure 12, 1753–1761.PubMedCrossRefGoogle Scholar
  17. 17.
    Yao, J. (1981) On the application of phase relationships to complex structures. XVIII. RANTAN-random MULTAN. Acta. Cryst. A37, 642–644.Google Scholar
  18. 18.
    Westbrook, J. and Fitzgerald, P. M. (2003) The PDB format, mmCIF formats and other data formats. In: Structural Bioinformatics (Bourne, P. E. and Weissig, H., eds.), John Wiley and Sons, Inc., Hoboken, NJ, pp. 161–179.Google Scholar
  19. 19.
    Fan, H.-F., Woolfson, M. M., and Yao, J.-X. (1993) New techniques of applying multi-wavelength anomalous scattering data. Proc. R. Soc. Lond. A 442, 13–32.CrossRefGoogle Scholar
  20. 20.
    Sheldrick, G. M., Hauptman, H. A., Weeks, C. M., Miller, R., and Uson, I. (2001) Direct methods: ab initio phasing. In: International Tables for Macromolecular Crystallography, Vol. F (Rossmann, M. G., and Arnold, E., eds.), Kluwer Academic Publishers, Dordrecht, Germany, pp. 333–345.Google Scholar
  21. 21.
    Brünger, A. T. (1997) Free R value: cross-validation in crystallography. Meth. Enzym. 277, 366–396.PubMedCrossRefGoogle Scholar
  22. 22.
    De La Fortelle, E. and Bricogne, G. (1997) Maximum-likelihood heavy-atom parameter refinement for the multiple isomorphous replacement and multiwavelength anomalous diffraction methods, Meth. Enzym. 276, 472–494.CrossRefGoogle Scholar
  23. 23.
    Hendrickson, W. A. and Lattman, E. E. (1970) Representation of phase probability distributions for simplified combination of independent phase informaton. Acta Cryst. B26, 136–143.Google Scholar
  24. 24.
    Bricogne, G., Vonrhein, C., Flensburg, C., Schiltz, M., and Paciorek, W. (2003) Generation, representation and flow of phase information in structure determination: recent developments in and around SHARP 2.0. Acta Cryst. D59, 2023–2030.Google Scholar
  25. 25.
    Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G., and North, A. C. T. (1961) The structure of haemoglobin. VIII. A three-dimensional Fourier synthesis at 5.5 Å resolution: Determination of the phase angles. Proc. Roy. Soc. A 265, 15–38.CrossRefGoogle Scholar
  26. 26.
    Cowtan, K. D. and Zhang, K. Y. (1999) Density modification for macromolecular phase improvement. Prog. Biophys. Mol. Biol. 72, 245–270.PubMedCrossRefGoogle Scholar
  27. 27.
    Abrahams, J. P. and Leslie, A. G. W. (1996) Methods used in the structure determination of bovine mitochondrial F1 ATPase. Acta Cryst. D52, 30–42.Google Scholar
  28. 28.
    Perrakis, A., Morris, R. J., and Lamzin, V. S. (1999) Automated protein model building combined with iterative structure refinement. Nature Struct. Biol. 6, 458–463.PubMedCrossRefGoogle Scholar
  29. 29.
    Vonrhein, C. and Schulz, G. E. (1999). Locating proper non-crystallographic symmetry in low-resolution electron-density maps with the program GETAX. Acta Cryst. D55, 225–229.Google Scholar
  30. 30.
    Evans, G. and Pettifer, R. F. (2001) CHOOCH: a program for deriving anomalousscattering factors from X-ray fluorescence spectra. J. Appl. Cryst. 34, 82–86.CrossRefGoogle Scholar

Copyright information

© Humana Press Inc. 2007

Authors and Affiliations

  • Clemens Vonrhein
    • 1
  • Eric Blanc
    • 2
  • Pietro Roversi
    • 3
  • Gérard Bricogne
    • 1
  1. 1.Global Phasing Ltd.CambridgeUK
  2. 2.European Bioinformatics InstituteWellcome Trust Genome CampusCambridgeUK
  3. 3.Department of Biochemistry, Laboratory of Molecular BiophysicsUniversity of OxfordOxford

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