- PDB-4q69: Crystal structure of a SusD homolog (BT2259) from Bacteroides the... -
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基本情報
登録情報
データベース: PDB / ID: 4q69
タイトル
Crystal structure of a SusD homolog (BT2259) from Bacteroides thetaiotaomicron VPI-5482 at 2.50 A resolution
要素
Putative lipoprotein
キーワード
SUGAR BINDING PROTEIN / SusD-like_2 family / PF12771 / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 28-488 OF THE TARGET SEQUENCE.
解像度: 2.5→89.672 Å / Num. all: 51369 / Num. obs: 51369 / % possible obs: 100 % / 冗長度: 6.2 % / Rsym value: 0.155 / Net I/σ(I): 9
反射 シェル
Rmerge(I) obs: 0.01 / Diffraction-ID: 1
解像度 (Å)
冗長度 (%)
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
2.5-2.56
6.3
1.9
23643
3759
1.01
100
2.56-2.64
6.3
2.1
22941
3640
0.899
100
2.64-2.71
6.3
2.4
22387
3558
0.76
100
2.71-2.8
6.3
2.9
21907
3483
0.631
100
2.8-2.89
6.3
3.8
21098
3347
0.46
100
2.89-2.99
6.3
4.3
20516
3266
0.388
100
2.99-3.1
6.3
5.4
19757
3145
0.301
100
3.1-3.23
6.3
6.8
19016
3015
0.237
100
3.23-3.37
6.3
8.2
18211
2902
0.192
100
3.37-3.54
6.3
10.3
17595
2794
0.154
100
3.54-3.73
6.3
12.4
16667
2660
0.128
100
3.73-3.95
6.3
14.5
15747
2512
0.104
100
3.95-4.23
6.3
16.1
14817
2369
0.09
100
4.23-4.56
6.2
18.6
13686
2198
0.076
100
4.56-5
6.2
18.9
12787
2052
0.069
100
5-5.59
6.2
17.1
11464
1857
0.073
100
5.59-6.46
6.2
16.4
10175
1650
0.073
100
6.46-7.91
6.1
18.1
8497
1400
0.061
100
7.91-11.18
5.9
24.4
6609
1113
0.043
100
11.18-89.672
5.4
20.9
3505
649
0.043
98.1
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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
MolProbity
3beta29
モデル構築
PDB_EXTRACT
3.1
データ抽出
SHELX
位相決定
SHARP
位相決定
SCALA
3.3.20
データスケーリング
REFMAC
5.7.0032
精密化
MOSFLM
データ削減
SHELXD
位相決定
精密化
構造決定の手法: 多波長異常分散 / 解像度: 2.5→89.672 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 13.373 / SU ML: 0.145 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.277 / ESU R Free: 0.199 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 SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...詳細: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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. 6. CHLORIDE ION (CL), SODIUM IONS (NA), AND GLYCEROL (GOL) MOLECULE FROM PURIFICATION/CRYSTALLIZATION/CRYOPROTECTION SOLUTIONS ARE MODELED.
Rfactor
反射数
%反射
Selection details
Rfree
0.1989
2605
5.1 %
RANDOM
Rwork
0.172
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obs
0.1733
51309
99.83 %
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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