Literature DB >> 2206482

Slow-cooling protocols for crystallographic refinement by simulated annealing.

A T Brünger1, A Krukowski, J W Erickson.   

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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Year:  1990        PMID： 2206482     DOI： 10.1107/s0108767390002355

Source DB:  PubMed          Journal:  Acta Crystallogr A        ISSN： 0108-7673            Impact factor:   2.290


  96 in total

1.  Crystal structure and mechanism of histone acetylation of the yeast GCN5 transcriptional coactivator.

Authors:  R C Trievel; J R Rojas; D E Sterner; R N Venkataramani; L Wang; J Zhou; C D Allis; S L Berger; R Marmorstein
Journal:  Proc Natl Acad Sci U S A       Date:  1999-08-03       Impact factor: 11.205

2.  Structure of HAP1-PC7 bound to DNA: implications for DNA recognition and allosteric effects of DNA-binding on transcriptional activation.

Authors:  A K Lukens; D A King; R Marmorstein
Journal:  Nucleic Acids Res       Date:  2000-10-15       Impact factor: 16.971

3.  Topography of a 2.0 A structure of alpha1-antitrypsin reveals targets for rational drug design to prevent conformational disease.

Authors:  P R Elliott; X Y Pei; T R Dafforn; D A Lomas
Journal:  Protein Sci       Date:  2000-07       Impact factor: 6.725

4.  The crystal structure of yeast phenylalanine tRNA at 1.93 A resolution: a classic structure revisited.

Authors:  H Shi; P B Moore
Journal:  RNA       Date:  2000-08       Impact factor: 4.942

5.  Structure of variant 2 scorpion toxin from Centruroides sculpturatus Ewing.

Authors:  William J Cook; Alan Zell; Dean D Watt; Steven E Ealick
Journal:  Protein Sci       Date:  2002-03       Impact factor: 6.725

6.  Crystal structures of photosynthetic reaction center and high-potential iron-sulfur protein from Thermochromatium tepidum: thermostability and electron transfer.

Authors:  T Nogi; I Fathir; M Kobayashi; T Nozawa; K Miki
Journal:  Proc Natl Acad Sci U S A       Date:  2000-12-05       Impact factor: 11.205

7.  Stabilization of penicillin G acylase from Escherichia coli: site-directed mutagenesis of the protein surface to increase multipoint covalent attachment.

Authors:  Olga Abian; Valeria Grazú; Juan Hermoso; Ramón González; José Luis García; Roberto Fernández-Lafuente; José Manuel Guisán
Journal:  Appl Environ Microbiol       Date:  2004-02       Impact factor: 4.792

8.  Assigning the protonation states of the key aspartates in β-Secretase using QM/MM X-ray structure refinement.

Authors:  Ning Yu; Seth A Hayik; Bing Wang; Ning Liao; Charles H Reynolds; Kenneth M Merz
Journal:  J Chem Theory Comput       Date:  2006       Impact factor: 6.006

9.  Structural prototypes for an extended family of flavoprotein reductases: comparison of phthalate dioxygenase reductase with ferredoxin reductase and ferredoxin.

Authors:  C C Correll; M L Ludwig; C M Bruns; P A Karplus
Journal:  Protein Sci       Date:  1993-12       Impact factor: 6.725

10.  Crystal structure of lignin peroxidase.

Authors:  S L Edwards; R Raag; H Wariishi; M H Gold; T L Poulos
Journal:  Proc Natl Acad Sci U S A       Date:  1993-01-15       Impact factor: 11.205
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