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Crystallography: Difference between revisions
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→Understanding and extending the properties and limitations of crystallographic computations
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== Understanding and extending the properties and limitations of crystallographic computations == | == Understanding and extending the properties and limitations of crystallographic computations == | ||
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=== Ensemble refinement, and molecular dynamics === | |||
# Burling et al. 1996 | # Burling et al. 1996 | ||
# | # Heterogeneity and Inaccuracy in Protein Structures Solved by X-Ray Crystallography. DePristo MA,de Bakker PIW, Blundell TL (2004) Structure 12, 831-838 [http://dx.doi.org/10.1016/j.str.2004.02.031] | ||
# Ensemble Refinement of Protein Crystal Structures: Validation and Application. Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN, Structure 15, 1040 - 1052 [http://dx.doi.org/10.1016/j.str.2007.06.019] | |||
# A comparison between molecular dynamics and X-ray results for dissociated CO in myoglobin. Vitkup D, Petsko GA, Karplus M. Nature Structural Biology 4, 202 - 208 (1997) [http://dx.doi.org/10.1038/nsb0397-202] (Vitkup et al showed that fitting a single model to MD-simulation derived "data" gave ~20% R, which means multiple conformers are sufficient to explain the "R-Factor Gap" between the 20% usually obtained for macromolecules, and the 5% routinely obtained for small molecules) | |||
=== | === Electron microscopy and X-ray === | ||
# | # Elucidating the medium-resolution structure of ribosomal particles: an interplay between electron cryo-microscopy and X-ray crystallography. Harms J, Tocilj A, Levin I, Agmon I, Stark H, Kölln I, van Heel M, Cuff M, Schlünzen F, Bashan A, Franceschi F, Yonath A. Structure 7, 931-941 (1999) [http://dx.doi.org/10.1016/S0969-2126(99)80120-8] | ||
=== | === NMR versus X-ray === | ||
A couple of papers analysing and comparing NMR and X-ray methods/structures: | A couple of papers analysing and comparing NMR and X-ray methods/structures: | ||
# Science (1992), vol. 257, p. 961 | # Science (1992), vol. 257, p. 961 | ||
# X-ray Crystallography and NMR: Complementary Views of Structure and Dynamics, Nature Structural Biology 4, 862-865 (1997). Preprint [http://atbweb.stanford.edu/scripts/papers.php?sendfile=162 available] from Axel Brunger's "publications" website. | # X-ray Crystallography and NMR: Complementary Views of Structure and Dynamics, Nature Structural Biology 4, 862-865 (1997). Preprint [http://atbweb.stanford.edu/scripts/papers.php?sendfile=162 available] from Axel Brunger's "publications" website. | ||
# Traditional Biomolecular Structure Determination by NMR Spectroscopy Allows for Major Errors. S.B. Nabuurs, C.A.E.M. Spronk, G.W. Vuister, G. Vriend. PLoS Comput Biol 2(2): e9. http://dx.doi.org/10.1371/journal.pcbi.0020009 | # Traditional Biomolecular Structure Determination by NMR Spectroscopy Allows for Major Errors. S.B. Nabuurs, C.A.E.M. Spronk, G.W. Vuister, G. Vriend. PLoS Comput Biol 2(2): e9. http://dx.doi.org/10.1371/journal.pcbi.0020009 | ||