- PDB-4o2t: Crystal structure of a DUF4827 family protein (BDI_1692) from Par... -
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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: 4o2t
タイトル
Crystal structure of a DUF4827 family protein (BDI_1692) from Parabacteroides distasonis ATCC 8503 at 2.40 A resolution
要素
Uncharacterized protein
キーワード
STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PF16109 family / DUF4827 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
機能・相同性
Protein of unknown function DUF4827 / Domain of unknown function (DUF4827) / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / Roll / Alpha Beta / Uncharacterized protein
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 WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 24-190 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
0.97953
1
3
0.97903
1
反射
解像度: 2.4→29.673 Å / Num. obs: 19613 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 66.457 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 12.07
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
2.39-2.48
0.664
1.6
10264
3014
76.6
2.48-2.57
0.509
2.2
11872
3381
99.9
2.57-2.69
0.365
3.1
13133
3810
99.8
2.69-2.83
0.263
4.2
11749
3643
99.5
2.83-3.01
0.162
7
13698
3799
99.9
3.01-3.24
0.106
10.6
13077
3688
99.7
3.24-3.57
0.069
15.7
12621
3756
99.4
3.57-4.08
0.049
21.5
11999
3616
98.1
4.08-5.12
0.041
25.6
12049
3623
98.1
5.12
0.03
27
12607
3727
97.8
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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
5.7.0032
精密化
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: 2.4→29.673 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 15.146 / SU ML: 0.174 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.291 / ESU R Free: 0.217 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.
Rfactor
反射数
%反射
Selection details
Rfree
0.2239
997
5.1 %
RANDOM
Rwork
0.1843
-
-
-
obs
0.1863
19570
99.41 %
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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