- PDB-4dwe: Crystal structure of a putative polysaccharide deacetylase (BACOV... -
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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: 4dwe
タイトル
Crystal structure of a putative polysaccharide deacetylase (BACOVA_03992) from Bacteroides ovatus ATCC 8483 at 2.01 A resolution
要素
uncharacterized protein
キーワード
Structural Genomics / Unknown Function / Hypothetical protein / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / CSAP
THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 21-499 OF THE TARGET SEQUENCE.
モノクロメーター: double 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
0.9796
1
3
0.97925
1
反射
解像度: 2.01→29.571 Å / Num. obs: 32317 / % possible obs: 97 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.32 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 7.17
反射 シェル
Diffraction-ID: 1
解像度 (Å)
最高解像度 (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
% possible all
2.01-2.08
0.437
1.8
10567
5721
95.2
2.08-2.17
0.344
2.3
13280
6571
98.1
2.17-2.26
0.271
2.8
11064
5494
97.9
2.26-2.38
0.236
3.3
12311
6103
97.2
2.38-2.53
0.203
3.8
12030
6050
97.3
2.53-2.73
0.154
4.9
11549
6064
95.6
2.73-3
0.111
6.8
12322
5962
98.1
3-3.43
0.07
10.6
12257
6003
97.7
3.43-4.32
0.042
16.2
11656
5962
95.8
4.32
0.037
19
12272
6028
96.6
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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
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
December29, 2011
データスケーリング
REFMAC
5.6.0117
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: 2.01→29.571 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.127 / SU ML: 0.102 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.148 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 SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...詳細: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS 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. GLYCEROL (GOL) MOLECULES FROM THE CRYSTALLIZATION SOLUTION ARE MODELED.
Rfactor
反射数
%反射
Selection details
Rfree
0.1936
1596
4.9 %
RANDOM
Rwork
0.1486
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-
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obs
0.1509
32268
98.78 %
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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