- PDB-3bhn: Crystal structure of a dj-1/pfpi-like protein (shew_2856) from sh... -
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基本情報
登録情報
データベース: PDB / ID: 3bhn
タイトル
Crystal structure of a dj-1/pfpi-like protein (shew_2856) from shewanella loihica pv-4 at 1.76 A resolution
要素
ThiJ/PfpI domain protein
キーワード
UNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
機能・相同性
DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / ThiJ/PfpI domain protein
解像度: 1.76→29.223 Å / Num. obs: 27863 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / 冗長度: 10.35 % / Biso Wilson estimate: 22.32 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 13.14
反射 シェル
解像度 (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Diffraction-ID
% possible all
1.76-1.82
0.806
2
26238
1
95.4
1.82-1.9
0.6
2.8
31636
1
100
1.9-1.98
0.436
4
26930
1
99.9
1.98-2.09
0.29
6.1
30581
1
100
2.09-2.22
0.193
8.8
28768
1
100
2.22-2.39
0.139
11.8
28798
1
100
2.39-2.63
0.101
15.3
29162
1
100
2.63-3.01
0.072
20
28919
1
99.9
3.01-3.78
0.05
27.6
28654
1
100
3.78-29.223
0.044
32.6
28499
1
99
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位相決定
位相決定
手法: 多波長異常分散
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解析
ソフトウェア
名称
バージョン
分類
NB
REFMAC
5.2.0019
精密化
PHENIX
精密化
SOLVE
位相決定
MolProbity
3beta29
モデル構築
XSCALE
データスケーリング
PDB_EXTRACT
3
データ抽出
ADSC
Quantum
データ収集
XDS
データ削減
精密化
構造決定の手法: 多波長異常分散 / 解像度: 1.76→29.223 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.797 / SU ML: 0.061 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.091 立体化学のターゲット値: MAXIMUM LIKELIHOOD WITH PHASES 詳細: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...詳細: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. 1,2-ETHANEDIOL MOLECULES FROM THE CRYSTALLIZATION CONDITIONS HAVE BEEN MODELED IN THE SOLVENT STRUCTURE.
Rfactor
反射数
%反射
Selection details
Rfree
0.19
1398
5 %
RANDOM
Rwork
0.162
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-
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obs
0.163
27782
99.88 %
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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: 1.2 Å / 溶媒モデル: MASK