Hostname: page-component-78c5997874-fbnjt Total loading time: 0 Render date: 2024-11-10T16:06:25.807Z Has data issue: false hasContentIssue false
  • English
  • Français

Protein refinement with GSAS-II

Published online by Cambridge University Press:  26 April 2019

Robert Von Dreele
Robert Von Dreele*
Affiliation:
Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439
*
a)Author to whom correspondence should be addressed. Electronic mail: vondreele@anl.gov
Get access Rights & Permissions [Opens in a new window]

Abstract

The General Structure Analysis System (GSAS)-II software package is a fully developed, open source, crystallographic data analysis system written almost entirely in Python. For powder diffraction, it encompasses the entire data analysis process beginning with 2-dimensonal image integration, peak selection, fitting and indexing, followed by intensity extraction, structure solution and ultimately Rietveld refinement, all driven by an intuitive graphical interface. Significant functionality of GSAS-II also can be scripted to allow it to be integrated into workflows or other software. For protein studies, it includes restraints on bond distances, angles, torsions, chiral volumes and coupled torsions (e.g. Ramachandran Φ/Ψ angles) each with graphical displays allowing visual validation. Each amino acid residue (and any ligands) can be represented by flexible rigid bodies with refinable internal torsions and optionally fully described TLS thermal motion. The least-squares algorithm invokes a Levenberg-Marquart minimization of a normalized double precision full matrix via Singular Value Decomposition providing fast convergence and high stability even for a large number of parameters. This paper will focus on the description of the flexible rigid body model of the protein and the details of the refinement algorithm.

Keywords

proteinpowder diffractionpython
Type
Technical Articles
Information
Powder Diffraction , Volume 34 , Supplement S1 , September 2019 , pp. S32 - S35
Copyright
Copyright © International Centre for Diffraction Data 2019 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Colovos, C. and Yeates, T. O. (1993). “Verification of protein structures: patterns of nonbonded atomic interactions,” Protein Sci. 2, 1511–1519.Google Scholar
Emsley, P., Lohkamp, B., Scott, W., and Cowtan, K. (2010). “Features and development of coot,” Acta Cryst. D66, 486–501.Google Scholar
Fong, K., Jefferson, T., Suyehiro, T., and Walton, L. (1993). Guide to the SLATEC Common Mathematical Library. http://www.netlib.org/slatec.Google Scholar
Larson, A. C. and Von Dreele, R. B. (2004). GSAS General Structure Analysis System. Report LAUR 86-748, Los Alamos National Laboratory.Google Scholar
Laskowski, R. A., MacArthur, M. W., Moss, D. S., and Thornton, J. M. (1993). “PROCHECK: a program to check the stereochemical quality of protein structures,” J. Appl. Cryst. 26, 283–291.Google Scholar
Margiolaki, I., Giannopoulou, A. E., Wright, J. P., Knight, L., Norrman, M., Schluckebier, G., Fitch, A. N., and Von Dreele, R. B. (2013). “High-resolution powder X-ray data reveal the T6 hexameric form of bovine insulin,” Acta Cryst. D69, 978–990.Google Scholar
Press, W. H., Flannery, B. P., Teukolsky, S. A., and Vettering, W. T. (1987). Numerical Recipes – The Art of Scientific Computing (Cambridge Univ. Press, Cambridge).Google Scholar
Rietveld, H. M. (1969). “A profile refinement method for nuclear and magnetic structures,” J. Appl. Crystallogr. 2, 65–71.Google Scholar
Shoemaker, V. and Trueblood, K. N. (1968). “On the rigid-body motion of molecules in crystals,” Acta Cryst. B24, 63–76.Google Scholar
Toby, B. H. and Von Dreele, R. B. (2013). “GSAS-II : the genesis of a modern open-source all purpose crystallography software package”, J. Appl. Cryst. 46, 544–549.Google Scholar
Toby, B. H. and Von Dreele, R. B. (2014). “What's new in GSAS-II,” Powder Diffr. 29, S2–S6.Google Scholar
Von Dreele, R. B. (1999). “Combined Rietveld and stereochemical restraint refinement of a protein crystal structure,” J. Appl. Cryst. 32, 1084–1089.Google Scholar
Von Dreele, R. B. (2001). “Binding of N-acetylglucosamine to chicken egg lysozyme: a powder diffraction study,” Acta Cryst. D57, 1836–1842.Google Scholar
Von Dreele, R. B. (2005). “Binding of N-acetylglucosamine oligosaccharides to hen egg-white lysozyme: a powder diffraction study,” Acta Cryst. D61, 22–32.Google Scholar
Von Dreele, R. B., Stephens, P. W., Blessing, R. H., and Smith, G. W. (2000). “The first protein crystal structure determined from high-resolution X-ray powder diffraction data: a variant of T3R3 human insulin-zinc complex produced by grinding,” Acta Cryst. D56, 1549–1553.Google Scholar