Flat bulk-solvent model: obtaining optimal parameters

被引：37

作者：

Fokine, A ^{[1
]}

Urzhumtsev, A ^{[1
]}

机构：

[1] Univ Nancy 1, Fac Sci, CNRS, UPRESA 7036, F-54506 Vandoeuvre Les Nancy, France

来源：

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY | 2002年 / 58卷

关键词：

D O I：

10.1107/S0907444902010284

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

A bulk-solvent correction is regularly used for macromolecular refinement. The flat model of the bulk solvent is considered to be the most reliable. It is shown that the standard procedure does not always result in the optimal values of the bulk-solvent correction parameters. A method to obtain the best values for parameters k(sol) and B-sol of the flat-solvent model is discussed. The values of correctly determined parameters for crystallographic structures deposited in the Protein Data Bank are clustered around k(sol) = 0.35 e Angstrom(-3) and B-sol = 46 Angstrom(2), which have a reasonable physical meaning. Such a distribution allows the use of these mean values of solvent parameters for many practical applications when refined parameters cannot be obtained, especially when an atomic model in the unit cell is not yet known.

引用

页码：1387 / 1392

页数：6

共 17 条

[1] Modeling and refinement of water molecules and disordered solvent
Badger, J
[J]. MACROMOLECULAR CRYSTALLOGRAPHY, PT B, 1997, 277 : 344 - 352
[2] PROTEIN DATA BANK - COMPUTER-BASED ARCHIVAL FILE FOR MACROMOLECULAR STRUCTURES
BERNSTEIN, FC
KOETZLE, TF
WILLIAMS, GJB
MEYER, EF
BRICE, MD
RODGERS, JR
KENNARD, O
SHIMANOUCHI, T
TASUMI, M
[J]. JOURNAL OF MOLECULAR BIOLOGY, 1977, 112 (03) : 535 - 542
[3] Crystallography & NMR system:: A new software suite for macromolecular structure determination
Brunger, AT
Adams, PD
Clore, GM
DeLano, WL
Gros, P
Grosse-Kunstleve, RW
Jiang, JS
Kuszewski, J
Nilges, M
Pannu, NS
Read, RJ
Rice, LM
Simonson, T
Warren, GL
[J]. ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 1998, 54 : 905 - 921
[4] THE 3RD IGG-BINDING DOMAIN FROM STREPTOCOCCAL PROTEIN-G - AN ANALYSIS BY X-RAY CRYSTALLOGRAPHY OF THE STRUCTURE ALONE AND IN A COMPLEX WITH FAB
DERRICK, JP
WIGLEY, DB
[J]. JOURNAL OF MOLECULAR BIOLOGY, 1994, 243 (05) : 906 - 918
[5] On the use of low-resolution data for translation search in molecular replacement
Fokine, A
Urzhumtsev, A
[J]. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES, 2002, 58 : 72 - 74
[6] FOKINE A, 2001, CCP4 NEWSL, V39, P71
[7] On the distribution of the bulk-solvent correction parameters
Glykos, NM
Kokkinidis, M
[J]. ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 2000, 56 : 1070 - 1072
[8] PROTEIN HYDRATION OBSERVED BY X-RAY-DIFFRACTION - SOLVATION PROPERTIES OF PENICILLOPEPSIN AND NEURAMINIDASE CRYSTAL-STRUCTURES
JIANG, JS
BRUNGER, AT
[J]. JOURNAL OF MOLECULAR BIOLOGY, 1994, 243 (01) : 100 - 115
[9] KOSTREWA D, 1997, CCP4 NEWSLETT, V34, P9
[10] LECOMTE C, 1999, NATO ASI EUROCONFE E, P23

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