- PDB-3cjl: Crystal structure of a protein of unknown function (eca1910) from... -
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基本情報
登録情報
データベース: PDB / ID: 3cjl
タイトル
Crystal structure of a protein of unknown function (eca1910) from pectobacterium atrosepticum scri1043 at 2.20 A resolution
要素
Domain of unknown function
キーワード
UNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
機能・相同性
Protein of unknown function DUF3861 / Protein of unknown function DUF3861 / DUF3861 domain superfamily / Domain of Unknown Function with PDB structure (DUF3861) / Ubiquitin-like (UB roll) / Roll / Alpha Beta / Uncharacterized protein
THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
モノクロメーター: Double crystal / プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長
波長: 0.97908 Å / 相対比: 1
反射
解像度: 2.2→29.123 Å / Num. obs: 14004 / % possible obs: 99.9 % / 冗長度: 7.3 % / Biso Wilson estimate: 39.316 Å2 / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Net I/σ(I): 5.1
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
2.2-2.26
7.4
0.716
1.1
7582
1022
0.716
100
2.26-2.32
7.5
0.611
1.3
7596
1017
0.611
100
2.32-2.39
7.5
0.487
1.6
7068
948
0.487
100
2.39-2.46
7.4
0.416
1.9
7240
973
0.416
100
2.46-2.54
7.5
0.348
2.2
6727
899
0.348
100
2.54-2.63
7.4
0.282
2.7
6562
882
0.282
100
2.63-2.73
7.5
0.229
3.4
6523
874
0.229
100
2.73-2.84
7.5
0.183
4.2
6038
809
0.183
100
2.84-2.97
7.5
0.164
4.6
5954
799
0.164
100
2.97-3.11
7.5
0.129
5.7
5755
768
0.129
100
3.11-3.28
7.4
0.111
6.4
5398
727
0.111
100
3.28-3.48
7.4
0.092
7.4
5047
683
0.092
100
3.48-3.72
7.4
0.082
8.1
4727
642
0.082
100
3.72-4.02
7.3
0.073
9.1
4350
593
0.073
100
4.02-4.4
7.2
0.07
9.8
4060
563
0.07
100
4.4-4.92
7.2
0.068
9.4
3555
497
0.068
100
4.92-5.68
6.8
0.079
8.1
3101
457
0.079
100
5.68-6.96
6.3
0.09
7.2
2431
383
0.09
100
6.96-9.84
6.1
0.065
9.2
1837
302
0.065
100
9.84-29.123
5.6
0.065
9.1
930
166
0.065
94.8
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位相決定
位相決定
手法: 単波長異常分散
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解析
ソフトウェア
名称
バージョン
分類
NB
REFMAC
5.2.0019
精密化
PHENIX
精密化
SOLVE
位相決定
MolProbity
3beta29
モデル構築
SCALA
データスケーリング
PDB_EXTRACT
3
データ抽出
MAR345
CCD
データ収集
MOSFLM
データ削減
精密化
構造決定の手法: 単波長異常分散 / 解像度: 2.2→29.123 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 9.998 / SU ML: 0.125 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.194 / ESU R Free: 0.164 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 RECORD CONTAINS RESIDUAL B FACTORS ONLY.
Rfactor
反射数
%反射
Selection details
Rfree
0.22
695
5 %
RANDOM
Rwork
0.194
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obs
0.195
13985
99.94 %
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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