- PDB-4poi: Crystal structure of a putative periplasmic protein (BACCAC_02096... -
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IDまたはキーワード:
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基本情報
登録情報
データベース: PDB / ID: 4poi
タイトル
Crystal structure of a putative periplasmic protein (BACCAC_02096) from Bacteroides caccae ATCC 43185 at 2.30 A resolution
要素
Putative periplasmic protein
キーワード
STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Two copies of DUF2874 domain (PF11396) / BLIP-like fold / 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 23-150 OF THE TARGET SEQUENCE.
モノクロメーター: single crystal Si(111) bent / 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
0.97895
1
反射
解像度: 2.3→46.904 Å / Num. obs: 14400 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / 冗長度: 8.56 % / Biso Wilson estimate: 46.34 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 38.15
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 obs
Num. unique obs
% possible all
2.3-2.38
8.8
0.275
7.44
12012
1353
99.9
2.38-2.48
0.206
10.1
13178
1489
99.9
2.48-2.59
0.165
11.9
11627
1370
99.9
2.59-2.73
0.118
16.1
11796
1437
100
2.73-2.9
0.081
24
13108
1424
100
2.9-3.12
0.056
33.8
12586
1400
100
3.12-3.43
0.035
50.2
12609
1423
100
3.43-3.93
0.03
59
10988
1452
99
3.93-4.93
0.021
81.2
12900
1458
99.8
4.93-46.9
0.021
80.2
12452
1594
98.7
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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
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
XSCALE
データスケーリング
REFMAC
5.8.0049
精密化
XDS
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: 2.3→46.904 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.885 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 13.944 / SU ML: 0.18 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.337 / ESU R Free: 0.249 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. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 3. WATERS WERE ...詳細: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 3. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 4. 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.
Rfactor
反射数
%反射
Selection details
Rfree
0.2788
722
5 %
RANDOM
Rwork
0.2436
-
-
-
obs
0.2453
14376
99.8 %
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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