Efficient anisotropic refinement of macromolecular structures using FFT - PubMed (original) (raw)
. 1999 Jan;55(Pt 1):247-55.
doi: 10.1107/S090744499801405X. Epub 1999 Jan 1.
Affiliations
- PMID: 10089417
- DOI: 10.1107/S090744499801405X
Efficient anisotropic refinement of macromolecular structures using FFT
G N Murshudov et al. Acta Crystallogr D Biol Crystallogr. 1999 Jan.
Abstract
This paper gives the equations for the use of fast Fourier transformations in individual atomic anisotropic refinement. Restraints on bonded atoms, on the sphericity of each atom and between non-crystallographic symmetry related atoms are described. These have been implemented in the program REFMAC and its performance with several examples is analysed. All the tests show that anisotropic refinement not only reduces the R value and Rfree but also improves the fit to geometric targets, indicating that this parameterization is valuable for improving models derived from experimental data. The computer time taken is comparable to that for isotropic refinements.
Similar articles
- SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model.
Vaguine AA, Richelle J, Wodak SJ. Vaguine AA, et al. Acta Crystallogr D Biol Crystallogr. 1999 Jan;55(Pt 1):191-205. doi: 10.1107/S0907444998006684. Epub 1999 Jan 1. Acta Crystallogr D Biol Crystallogr. 1999. PMID: 10089410 - Cross-validation tests of time-averaged molecular dynamics refinements for determination of protein structures by X-ray crystallography.
Clarage JB, Phillips GN Jr. Clarage JB, et al. Acta Crystallogr D Biol Crystallogr. 1994 Jan 1;50(Pt 1):24-36. doi: 10.1107/S0907444993009515. Acta Crystallogr D Biol Crystallogr. 1994. PMID: 15299473 - Refinement of protein crystal structures using energy restraints derived from linear-scaling quantum mechanics.
Yu N, Yennawar HP, Merz KM Jr. Yu N, et al. Acta Crystallogr D Biol Crystallogr. 2005 Mar;61(Pt 3):322-32. doi: 10.1107/S0907444904033669. Epub 2005 Feb 24. Acta Crystallogr D Biol Crystallogr. 2005. PMID: 15735343 - Recent developments for crystallographic refinement of macromolecules.
Brünger AT. Brünger AT. Methods Mol Biol. 1996;56:245-66. doi: 10.1385/0-89603-259-0:245. Methods Mol Biol. 1996. PMID: 8781249 Review. No abstract available. - ACORN: a review.
Yao JX, Dodson EJ, Wilson KS, Woolfson MM. Yao JX, et al. Acta Crystallogr D Biol Crystallogr. 2006 Aug;62(Pt 8):901-8. doi: 10.1107/S0907444906008122. Epub 2006 Jul 18. Acta Crystallogr D Biol Crystallogr. 2006. PMID: 16855307 Review.
Cited by
- The role of the oligosaccharide binding cleft of rice BGlu1 in hydrolysis of cellooligosaccharides and in their synthesis by rice BGlu1 glycosynthase.
Pengthaisong S, Withers SG, Kuaprasert B, Svasti J, Cairns JR. Pengthaisong S, et al. Protein Sci. 2012 Mar;21(3):362-72. doi: 10.1002/pro.2021. Epub 2012 Jan 31. Protein Sci. 2012. PMID: 22238157 Free PMC article. - A novel allosteric inhibitor of macrophage migration inhibitory factor (MIF).
Bai F, Asojo OA, Cirillo P, Ciustea M, Ledizet M, Aristoff PA, Leng L, Koski RA, Powell TJ, Bucala R, Anthony KG. Bai F, et al. J Biol Chem. 2012 Aug 31;287(36):30653-63. doi: 10.1074/jbc.M112.385583. Epub 2012 Jul 10. J Biol Chem. 2012. PMID: 22782901 Free PMC article. - Archaeal Connectase is a specific and efficient protein ligase related to proteasome β subunits.
Fuchs ACD, Ammelburg M, Martin J, Schmitz RA, Hartmann MD, Lupas AN. Fuchs ACD, et al. Proc Natl Acad Sci U S A. 2021 Mar 16;118(11):e2017871118. doi: 10.1073/pnas.2017871118. Proc Natl Acad Sci U S A. 2021. PMID: 33688044 Free PMC article. - Structural and functional characterization of a noncanonical nucleoside triphosphate pyrophosphatase from Thermotoga maritima.
Awwad K, Desai A, Smith C, Sommerhalter M. Awwad K, et al. Acta Crystallogr D Biol Crystallogr. 2013 Feb;69(Pt 2):184-93. doi: 10.1107/S0907444912044630. Epub 2013 Jan 18. Acta Crystallogr D Biol Crystallogr. 2013. PMID: 23385455 Free PMC article. - Challenging semi-bootstrapping molecular-replacement strategy reveals intriguing crystal packing of rhizavidin.
Meir A, Livnah O. Meir A, et al. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Apr 1;66(Pt 4):373-8. doi: 10.1107/S1744309110004112. Epub 2010 Mar 26. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010. PMID: 20383003 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources