SpringerProtocols: Abstract: 12. Automated Structure Solution With autoSHARP

12. Automated Structure Solution With autoSHARP

By: Clemens Vonrhein², Eric Blanc³, Pietro Roversi⁴, Gérard Bricogne²

Abstract

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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.

Affiliation(s): (2) Global Phasing Ltd., Sheraton House, Castle Park, Cambridge, UK
(3) European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
(4) Department of Biochemistry, Laboratory of Molecular Biophysics, University of Oxford, Oxford, UK

Book Title: Macromolecular Crystallography Protocols: Volume 2: Structure Determination

Series: Methods in Molecular Biology | Volume: 364 | Pub. Date: Feb-05-2007 | Page Range: 215-230 | DOI: 10.1385/1-59745-266-1:215

Subject: Protein Science

Key Words: SHARP - autoSHARP - automation - structure solution

References

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1.	Bourne, S. R. (1978) Unix time-sharing system: The Unix shell. Bell Sys. Tech. J. 57, 1971–1990.

2.	Wall, L., Christiansen, T., and Orwant, J. (2000) Programming Perl, 3rd ed., O’Reilly and Associates, Inc., Sebastopol, CA.

3.	Collaborative Computational Project, Number 4 (1994) The CCP4 suite: programs for protein crystallography. Acta Cryst. D50, 760–763.

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.

5.	Cromer, D. T. (1983) Calculation of anomalous scattering factors at arbitrary wavelengths. J. Appl. Cryst. 16, 437–438.

6.	Wilson, A. J. C. (1942) Determination of absolute from relative X-ray intensity. Nature 150, 151–152.

7.	Matthews, B. W. (1968) The solvent content of protein crystals. J. Mol. Biol. 33, 491–497.

8.	Rossmann, M. G. and Blow, D. M. (1962) The detection of sub-units within the crystallographic asymmetric unit. Acta Cryst. 15, 24–31.

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.

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.

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.

12.	Schneider, T. R. and Sheldrick, G. M. (2002) Substructure solution with SHELXD. Acta Cryst. D58, 1772–1779.

13.	Weeks, C. M. and Miller, R. (1999) The design and implementation of SnB v2.0. J. Appl. Cryst. 32, 120–124.

14.	Grosse-Kunstleve, R. W. and Adams, P. D. (2003). Substructure search procedures for macromolecular structures. Acta Cryst. D59, 1966–1973.

15.	Terwilliger, T. C. (2003) Automated structure solution, density modification and model building. Acta Cryst. D58, 1937–1940.

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.

17.	Yao, J. (1981) On the application of phase relationships to complex structures. XVIII. RANTAN-random MULTAN. Acta. Cryst. A37, 642–644.

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.

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.

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.

21.	Brünger, A. T. (1997) Free R value: cross-validation in crystallography. Meth. Enzym. 277, 366–396.

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.

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.

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.

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.

26.	Cowtan, K. D. and Zhang, K. Y. (1999) Density modification for macromolecular phase improvement. Prog. Biophys. Mol. Biol. 72, 245–270.

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.

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.

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.

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.

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