- PDB-2i02: CRYSTAL STRUCTURE OF a pyridoxamine 5'-phosphate oxidase-like fam... -
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基本情報
登録情報
データベース: PDB / ID: 2i02
タイトル
CRYSTAL STRUCTURE OF a pyridoxamine 5'-phosphate oxidase-like family protein (NPUN_R6570) FROM NOSTOC PUNCTIFORME PCC 73102 AT 1.80 A RESOLUTION
要素
general stress protein of COG3871
キーワード
OXIDOREDUCTASE / GENERAL STRESS PROTEIN OF COG3871 / PYRIDOXAMINE 5'-PHOSPHATE OXIDASE-LIKE FAMILY PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
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
0.979197
1
2
0.91837
1
反射
解像度: 1.8→29.921 Å / Num. obs: 32823 / % possible obs: 100 % / 冗長度: 10.3 % / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Net I/σ(I): 4.8
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
1.8-1.85
10.6
0.946
0.8
25296
2377
0.946
100
1.85-1.9
10.6
0.731
1.1
24511
2311
0.731
100
1.9-1.95
10.6
0.543
1.4
24005
2262
0.543
100
1.95-2.01
10.6
0.435
1.8
23213
2187
0.435
100
2.01-2.08
10.6
0.36
2.1
22570
2136
0.36
100
2.08-2.15
10.6
0.303
2.5
21862
2068
0.303
100
2.15-2.23
10.6
0.255
3
20934
1983
0.255
100
2.23-2.32
10.5
0.205
3.7
20335
1938
0.205
100
2.32-2.43
10.4
0.181
4.2
19221
1842
0.181
100
2.43-2.55
10.5
0.161
4.7
18552
1772
0.161
100
2.55-2.68
10.4
0.134
5.5
17591
1694
0.134
100
2.68-2.85
10.3
0.113
6.5
16658
1610
0.113
100
2.85-3.04
10.3
0.086
8.1
15668
1527
0.086
100
3.04-3.29
10.2
0.079
8.2
14363
1413
0.079
100
3.29-3.6
10
0.075
8.2
13195
1314
0.075
100
3.6-4.02
9.7
0.067
8.9
11638
1200
0.067
100
4.02-4.65
9
0.07
8.3
9675
1074
0.07
100
4.65-5.69
9.7
0.065
8.9
8980
925
0.065
100
5.69-8.05
9.9
0.057
11.2
7313
741
0.057
100
8.05-29.92
8.5
0.045
12.3
3829
449
0.045
98.2
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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
SHELX
位相決定
REFMAC
5.2.0019
精密化
SCALA
データスケーリング
PDB_EXTRACT
2
データ抽出
MOSFLM
データ削減
CCP4
(SCALA)
データスケーリング
SHELXD
位相決定
SHARP
位相決定
精密化
構造決定の手法: 多波長異常分散 / 解像度: 1.8→29.921 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.503 / SU ML: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.107 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. RESIDUES A1-4, A46-48, B1-4, AND B136-138 ARE DISORDERED AND NOT INCLUDED IN THE MODEL. 4. RESIDUES B45-48 AND B61 ARE POORLY ORDERED. 5. MOLECULES FMN AND PEG-300 (P33) ARE MODELED. 6. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 7. UNEXPLAINED DENSITY OBSERVED NEAR RESIDUES A58, A98, A101, B31-32, B61, B67.
Rfactor
反射数
%反射
Selection details
Rfree
0.204
1663
5.1 %
RANDOM
Rwork
0.177
-
-
-
all
0.178
-
-
-
obs
-
32793
99.99 %
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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