- PDB-3kop: Crystal structure of Protein with a cyclophilin-like fold (YP_831... -
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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: 3kop
タイトル
Crystal structure of Protein with a cyclophilin-like fold (YP_831253.1) from Arthrobacter sp. FB24 at 1.90 A resolution
要素
Uncharacterized protein
キーワード
Structural Genomics / Unknown function / Protein with a cyclophilin-like fold / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
機能・相同性
Protein of unknown function DUF3830 / Protein of unknown function (DUF3830) / Cyclophilin - #20 / Cyclophilin / Cyclophilin-like domain superfamily / Beta Barrel / Mainly Beta / Uncharacterized protein
A: Uncharacterized protein B: Uncharacterized protein C: Uncharacterized protein D: Uncharacterized protein E: Uncharacterized protein F: Uncharacterized protein
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
0.91837
1
2
0.97963
1
反射
解像度: 1.9→29.907 Å / Num. obs: 88263 / % possible obs: 99.5 % / 冗長度: 2.6 % / Biso Wilson estimate: 18.599 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 9
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
1.9-1.95
2.5
0.498
2
16367
6518
0.498
100
1.95-2
2.5
0.399
1.9
16215
6414
0.399
99.9
2-2.06
2.5
0.313
2.4
15622
6195
0.313
100
2.06-2.12
2.5
0.302
0.9
15339
6075
0.302
100
2.12-2.19
2.5
0.224
3.4
14709
5797
0.224
99.9
2.19-2.27
2.5
0.215
1.3
14349
5664
0.215
99.9
2.27-2.36
2.5
0.173
4.3
13863
5442
0.173
99.9
2.36-2.45
2.6
0.143
5.2
13407
5245
0.143
99.8
2.45-2.56
2.6
0.126
5.9
12792
5008
0.126
99.7
2.56-2.69
2.6
0.111
6.2
12198
4782
0.111
99.6
2.69-2.83
2.6
0.089
8
11708
4564
0.089
99.5
2.83-3
2.6
0.08
8.5
11149
4330
0.08
99.4
3-3.21
2.6
0.071
8.9
10343
4029
0.071
99.2
3.21-3.47
2.6
0.057
10.5
9722
3773
0.057
99.2
3.47-3.8
2.6
0.047
12.8
8962
3462
0.047
98.8
3.8-4.25
2.6
0.041
12.6
8129
3136
0.041
98.6
4.25-4.91
2.6
0.036
16.2
7106
2731
0.036
98.2
4.91-6.01
2.6
0.037
16.2
6067
2334
0.037
98
6.01-8.5
2.6
0.045
13
4682
1797
0.045
97.5
8.5-29.91
2.6
0.041
12.3
2479
967
0.041
94.4
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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
SOLVE
位相決定
MolProbity
3beta29
モデル構築
SCALA
3.2.5
データスケーリング
PDB_EXTRACT
3.006
データ抽出
MOSFLM
データ削減
精密化
構造決定の手法: 多波長異常分散 / 解像度: 1.9→29.907 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 6.209 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.121 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.
Rfactor
反射数
%反射
Selection details
Rfree
0.196
4416
5 %
RANDOM
Rwork
0.16
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-
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obs
0.162
88235
99.3 %
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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