ジャーナル: PLoS Biol / 年: 2010 タイトル: Complete structural model of Escherichia coli RNA polymerase from a hybrid approach. 著者: Natacha Opalka / Jesse Brown / William J Lane / Kelly-Anne F Twist / Robert Landick / Francisco J Asturias / Seth A Darst / 要旨: The Escherichia coli transcription system is the best characterized from a biochemical and genetic point of view and has served as a model system. Nevertheless, a molecular understanding of the ...The Escherichia coli transcription system is the best characterized from a biochemical and genetic point of view and has served as a model system. Nevertheless, a molecular understanding of the details of E. coli transcription and its regulation, and therefore its full exploitation as a model system, has been hampered by the absence of high-resolution structural information on E. coli RNA polymerase (RNAP). We use a combination of approaches, including high-resolution X-ray crystallography, ab initio structural prediction, homology modeling, and single-particle cryo-electron microscopy, to generate complete atomic models of E. coli core RNAP and an E. coli RNAP ternary elongation complex. The detailed and comprehensive structural descriptions can be used to help interpret previous biochemical and genetic data in a new light and provide a structural framework for designing experiments to understand the function of the E. coli lineage-specific insertions and their role in the E. coli transcription program.
プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長
波長: 0.9919 Å / 相対比: 1
反射
解像度: 1.6→25 Å / Num. obs: 42737 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / 冗長度: 7 % / Rsym value: 0.069 / Net I/σ(I): 40
反射 シェル
解像度: 1.6→1.64 Å / 冗長度: 6.5 % / Mean I/σ(I) obs: 5.1 / Rsym value: 0.416 / % possible all: 94
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解析
ソフトウェア
名称
バージョン
分類
MAR345dtb
データ収集
SHARP
位相決定
REFMAC
5.5.0091
精密化
HKL-2000
データ削減
HKL-2000
データスケーリング
精密化
構造決定の手法: 単波長異常分散 / 解像度: 1.6→14.98 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.915 / SU B: 2.653 / SU ML: 0.084 / 交差検証法: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.094 立体化学のターゲット値: MAXIMUM LIKELIHOOD WITH PHASES 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
反射数
%反射
Selection details
Rfree
0.22955
1398
3.2 %
RANDOM
Rwork
0.20791
-
-
-
obs
0.20884
42737
98.5 %
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溶媒の処理
イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.4 Å / 溶媒モデル: MASK