- PDB-3g14: Crystal structure of nitroreductase family protein (YP_877874.1) ... -
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IDまたはキーワード:
読み込み中...
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基本情報
登録情報
データベース: PDB / ID: 3g14
タイトル
Crystal structure of nitroreductase family protein (YP_877874.1) from Clostridium novyi NT at 1.75 A resolution
要素
Nitroreductase family protein
キーワード
OXIDOREDUCTASE / YP_877874.1 / nitroreductase family protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
モノクロメーター: Single crystal Si(111) bent (horizontal focusing) プロトコル: MAD / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長
ID
波長 (Å)
相対比
1
0.91837
1
2
0.97876
1
3
0.97826
1
反射
解像度: 1.75→28.194 Å / Num. obs: 34941 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.426 Å2 / Rmerge(I) obs: 0.056
反射 シェル
解像度 (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
1.75-1.81
0.499
1.4
9468
5956
1
90.2
1.81-1.89
0.346
2
11911
7511
1
98.6
1.89-1.97
0.235
2.9
10013
6279
1
98.8
1.97-2.07
0.189
3.7
10432
6527
1
98.6
2.07-2.2
0.124
5.4
10967
6846
1
98.6
2.2-2.37
0.095
7
11049
6865
1
98.4
2.37-2.61
0.067
9.3
11008
6817
1
98.3
2.61-2.99
0.049
12.2
11041
6775
1
97.9
2.99-3.76
0.034
17
10889
6648
1
96.9
3.76-28.194
0.026
22.2
10969
6625
1
95.4
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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
SHELX
位相決定
MolProbity
3beta29
モデル構築
XSCALE
データスケーリング
PDB_EXTRACT
3.006
データ抽出
MAR345
CCD
データ収集
XDS
データ削減
SHELXD
位相決定
autoSHARP
位相決定
精密化
構造決定の手法: 多波長異常分散 / 解像度: 1.75→28.194 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 5.021 / SU ML: 0.081 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.12 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. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...詳細: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. SULFATE (SO4), ACETATE (ACT) IONS AND GLYCEROL (GOL) MOLECULES FROM CRYSTALLIZATION CONDITION WERE MODELED. 5. RESIDUES 156-164 OF A CHAIN AND 157-163 OF B CHAIN WERE NOT VISIBLE IN THE ELECTRON DENSITIES. THEY WERE UNMODELED.
Rfactor
反射数
%反射
Selection details
Rfree
0.219
1754
5 %
RANDOM
Rwork
0.173
-
-
-
obs
0.176
34929
99.35 %
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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