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Slow-cooling protocols for crystallographic refinement by simulated annealing
Abstract
An improved protocol for crystallographic refinement by simulated annealing is presented. It consists of slow cooling starting at high temperatures. Tests of refinements of aspartate aminotransferase and procin pepsin show that the slow-cooling protocol produces lower R factors and better geometry than other protocols previously published. The influence of the temperature-control method, weighting, cooling rate and duration of the heating stage on the success of the slow-cooling protocol is studied. Analysis of the time course of the potential-energy fluctuations indicates no global changes in the state of order of the system. Fluctuations of the potential energy are interpreted as localized conformational changes during the course of the refinement.
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Cited by
Borgstahl, G. E. O., Parge, H. E., Hickey, M. J., Beyer, W. F., Hallewell, R. A., & Tainer, J. A. (1992) · Cell · doi:10.1016/0092-8674(92)90270-m · Cited by 472
A new pattern for helix–turn–helix recognition revealed by the PU.l ETS–domain–DNA complex
Kodandapani, R., Pio, F., Ni, C.-Z., Piccialli, G., Klemsz, M., McKercher, S., Maki, R. A., & Ely, K. R. (1996) · Nature · doi:10.1038/380456a0 · Cited by 315
Crystal Structure of Human RhoA in a Dominantly Active Form Complexed with a GTP Analogue
Ihara, K., Muraguchi, S., Kato, M., Shimizu, T., Shirakawa, M., Kuroda, S., Kaibuchi, K., & Hakoshima, T. (1998) · Journal of Biological Chemistry · doi:10.1074/jbc.273.16.9656 · Cited by 190
Structural Basis for Catalysis and Inhibition ofN-Glycan Processing Class I α1,2-Mannosidases
Vallée, F., Karaveg, K., Herscovics, A., Moremen, K. W., & Howell, P. L. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.m006927200 · Cited by 152
Structures of SAP-1 Bound to DNA Targets from the E74 and c-fos Promoters
Mo, Y., Vaessen, B., Johnston, K., & Marmorstein, R. (1998) · Molecular Cell · doi:10.1016/s1097-2765(00)80130-6 · Cited by 103
Metadata
- Authors
- Brünger, A. T., Krukowski, A., & Erickson, J. W.
- Venue
- Acta Crystallographica Section A Foundations of Crystallography
- Published
- 1990-07-01
- Volume
- 46
- Issue
- 7
- Pages
- 585-593
- ISSN
- 0108-7673 (ISSN-L)
- OpenAlex
- W2060448324
- Cited by
- 517
- References
- 0
- FWCI
- 21.25
- Type
- journal article
- Language
- en
- Open access
- closed
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
