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Crystallographic refinement by simulated annealing
Open accessAbstract
Crystallographic refinement by simulated annealing with molecular dynamics has been applied to a 2.8 A (1 A = 0.1 nm) resolution X-ray structure of aspartate aminotransferase. Comparison of the refined structure and a structure obtained by combined restrained least-squares refinement and manual re-fitting shows a similar R factor, stereochemistry, and mean difference from the isomorphous replacement phase centroids. Crystallographic refinement by simulated annealing accomplished structural changes and improvements of the electron density maps that were not possible by using restrained least-squares refinement without manual re-fitting. Crystallographic refinement by simulated annealing can generate an ensemble of structures, each of which agrees with the diffraction information. Regions of large variations of the ensemble indicate either erroneously fitted or disordered segments of the macromolecule.
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Citations
Cited by
Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination
Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J. S., Kuszewski, J., Nilges, M., Pannu, N. S., et al. (1998) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444998003254 · Cited by 15,715
Self-citationThe Xplor-NIH NMR molecular structure determination package
Schwieters, C. D., Kuszewski, J. J., Tjandra, N., & Marius Clore, G. (2003) · Journal of Magnetic Resonance · doi:10.1016/s1090-7807(02)00014-9 · Cited by 2,369
Atomic model of plant light-harvesting complex by electron crystallography
Kühlbrandt, W., Wang, D. N., & Fujiyoshi, Y. (1994) · Nature · doi:10.1038/367614a0 · Cited by 1,905
Rational design of potent sialidase-based inhibitors of influenza virus replication
von Itzstein, M., Wu, W.-Y., Kok, G. B., Pegg, M. S., Dyason, J. C., Jin, B., Van Phan, T., Smythe, M. L., White, H. F., Oliver, S. W., et al. (1993) · Nature · doi:10.1038/363418a0 · Cited by 1,862
Refined structure of the human histocompatibility antigen HLA-A2 at 2.6 Å resolution
Saper, M. A., Bjorkman, P. J., & Wiley, D. C. (1991) · Journal of Molecular Biology · doi:10.1016/0022-2836(91)90567-p · Cited by 1,077
Metadata
- Authors
- Brünger, A. T.
- Venue
- Journal of Molecular Biology
- Publisher
- Elsevier BV
- Published
- 1988-10
- Volume
- 203
- Issue
- 3
- Pages
- 803-816
- ISSN
- 0022-2836 (ISSN-L)
- OpenAlex
- W1993390869
- Cited by
- 404
- References
- 0
- FWCI
- 32.85
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Brünger, A. T. (1988). Crystallographic refinement by simulated annealing. Journal of Molecular Biology. https://doi.org/10.1016/0022-2836(88)90211-2
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