- PDB-3klb: Crystal structure of Putative Flavoprotein in Complex with FMN (Y... -
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基本情報
登録情報
データベース: PDB / ID: 3klb
タイトル
Crystal structure of Putative Flavoprotein in Complex with FMN (YP_213683.1) from Bacteroides fragilis NCTC 9343 at 1.75 A resolution
要素
Putative Flavoprotein
キーワード
FLAVOPROTEIN / Putative Flavoprotein in Complex with FMN / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
THE CONSTRUCT (1-161) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (1-161) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE FOLLOWED BY THE TARGET SEQUENCE.
解像度: 1.75→27.832 Å / Num. obs: 23388 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.346 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 17.33
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
0.732
1.9
14799
3959
1
94.2
1.81-1.89
0.517
2.7
18269
4815
1
99.7
1.89-1.97
0.352
3.9
15497
4069
1
99.7
1.97-2.07
0.239
5.8
16181
4237
1
99.9
2.07-2.2
0.166
8.4
16864
4403
1
99.7
2.2-2.37
0.119
11.3
16811
4384
1
99.6
2.37-2.61
0.093
14.5
17081
4430
1
99.8
2.61-2.99
0.059
21.7
17121
4430
1
99.8
2.99-3.76
0.026
41.6
16860
4355
1
99.7
3.76-27.832
0.019
59.9
17114
4420
1
99.4
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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
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→27.832 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.281 / SU ML: 0.057 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.087 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 RECORD CONTAINS RESIDUAL B FACTORS ONLY. (3). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING ...詳細: (1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2). ATOM RECORD CONTAINS 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. (4). A MODIFIED FMN RESTRAINTS DICTIONARY WAS USED DURING THE REFINEMENT TO ALLOW BENDING OF THE FMN RING ALONG THE N5-N10 VIRTUAL AXIS. THIS RESULTS IN AN IMPROVED FIT BETWEEN THE FMN COORDINATE MODEL AND ELECTRON DENSITY. (5). SODIUM ION (NA) AND GLYCEROL (GOL) MOLECULES FROM CRYSTALLIZATION, AND ETHYLENE GLYCOL (EDO) MOLECULES FROM CRYO CONDITION ARE MODELED.
Rfactor
反射数
%反射
Selection details
Rfree
0.179
1196
5.1 %
RANDOM
Rwork
0.148
-
-
-
obs
0.15
23346
99.76 %
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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: BABINET MODEL WITH MASK