- PDB-3g6i: Crystal structure of an outer membrane protein, part of a putativ... -
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基本情報
登録情報
データベース: PDB / ID: 3g6i
タイトル
Crystal structure of an outer membrane protein, part of a putative carbohydrate binding complex (bt_1022) from bacteroides thetaiotaomicron vpi-5482 at 1.93 A resolution
要素
Putative outer membrane protein, part of carbohydrate binding complex
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
Protein of unknown function DUF3826 / Protein of unknown function (DUF3826) / DI(HYDROXYETHYL)ETHER / Uncharacterized protein
THE CONSTRUCT (RESIDUES 20-222) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 20-222) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
解像度: 1.93→48.97 Å / Num. obs: 28120 / % possible obs: 100 % / Observed criterion σ(I): -3 / 冗長度: 10.8 % / Biso Wilson estimate: 34.847 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 14.99
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
1.93-2
1.556
1.5
19786
2766
1
100
2-2.08
0.983
2.5
19767
2741
1
100
2.08-2.17
0.597
4
19062
2637
1
100
2.17-2.29
0.418
5.6
20970
2904
1
100
2.29-2.43
0.459
7.9
25707
2714
1
100
2.43-2.62
0.486
11.2
40520
2809
1
100
2.62-2.88
0.296
15.9
39793
2785
1
100
2.88-3.3
0.147
23.5
39982
2852
1
100
3.3-4.15
0.075
34.4
38946
2856
1
100
4.15-48.97
0.05
39.5
40165
3073
1
99.7
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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
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: 1.93→48.97 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 5.967 / SU ML: 0.076 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.118 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. SULFATE AND PEG FRAGMENTS MODELED ARE PRESENT IN CRYSTALLIZATION CONDITIONS.
Rfactor
反射数
%反射
Selection details
Rfree
0.223
1409
5 %
RANDOM
Rwork
0.197
-
-
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obs
0.198
28048
99.95 %
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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