- PDB-3i10: Crystal structure of Putative glycerophosphoryl diester phosphodi... -
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基本情報
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データベース: PDB / ID: 3i10
タイトル
Crystal structure of Putative glycerophosphoryl diester phosphodiesterase (NP_812074.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.35 A resolution
SEQUENCE THIS CONSTRUCT (RESIDUES 25-301) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. ...SEQUENCE THIS CONSTRUCT (RESIDUES 25-301) 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 monochromator (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
0.97993
1
3
0.9792
1
反射
解像度: 1.35→29.05 Å / Num. obs: 61313 / % possible obs: 100 % / 冗長度: 3.6 % / Biso Wilson estimate: 10.639 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 9.7
反射 シェル
Diffraction-ID: 1
解像度 (Å)
冗長度 (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
1.35-1.39
3.1
0.59
1.9
14135
4503
0.59
100
1.39-1.42
3.6
0.525
2.3
15862
4379
0.525
100
1.42-1.46
3.6
0.438
2.8
15316
4212
0.438
100
1.46-1.51
3.6
0.359
3.4
15137
4151
0.359
100
1.51-1.56
3.7
0.29
4.3
14626
4001
0.29
100
1.56-1.61
3.7
0.253
4.9
14185
3875
0.253
100
1.61-1.67
3.7
0.212
5.8
13782
3762
0.212
100
1.67-1.74
3.7
0.183
6.9
13396
3641
0.183
100
1.74-1.82
3.7
0.146
8.6
12669
3449
0.146
100
1.82-1.91
3.7
0.114
10.5
12182
3301
0.114
100
1.91-2.01
3.7
0.092
12.5
11765
3182
0.092
100
2.01-2.13
3.7
0.078
14.2
11143
3030
0.078
100
2.13-2.28
3.7
0.078
16
10358
2806
0.078
100
2.28-2.46
3.7
0.079
18
9756
2649
0.079
100
2.46-2.7
3.7
0.067
19.2
8908
2415
0.067
100
2.7-3.02
3.7
0.056
20.5
8191
2227
0.056
100
3.02-3.49
3.7
0.046
22.9
7151
1958
0.046
100
3.49-4.27
3.6
0.043
25
6183
1700
0.043
100
4.27-6.04
3.6
0.043
24.3
4694
1317
0.043
100
6.04-29.05
3.3
0.045
23.2
2525
755
0.045
98.6
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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
5.5.0053
精密化
PHENIX
精密化
SHELX
位相決定
MolProbity
3beta29
モデル構築
SCALA
3.2.5
データスケーリング
PDB_EXTRACT
3.006
データ抽出
MOSFLM
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: 1.35→29.05 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 1.738 / SU ML: 0.032 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.051 / ESU R Free: 0.053 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 PROTEIN ...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. ACETATE (ACT), ETHYLENE GLYCOL (EDO), AND POLYETHYLENE GLYCOL (PEG) FROM THE CRYSTALLIZATION/CRYOPROTECTANT SOLUTIONS HAVE BEEN MODELED INTO THE SOLVENT STRUCTURE. 5. TLS GROUPS WERE ASSIGNED WITH THE AID OF THE TLSMD SERVER.
Rfactor
反射数
%反射
Selection details
Rfree
0.172
3109
5.1 %
RANDOM
Rwork
0.15
-
-
-
obs
0.151
61269
99.96 %
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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