- PDB-2nlv: CRYSTAL STRUCTURE OF A XISI-LIKE PROTEIN (AVA_3825) FROM ANABAENA... -
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基本情報
登録情報
データベース: PDB / ID: 2nlv
タイトル
CRYSTAL STRUCTURE OF A XISI-LIKE PROTEIN (AVA_3825) FROM ANABAENA VARIABILIS ATCC 29413 AT 1.30 A RESOLUTION
要素
XisI protein-like
キーワード
UNKNOWN FUNCTION / XISI-LIKE PROTEIN / STRUCTURAL GENOMICS (構造ゲノミクス) / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2 / PSI-Biology
機能・相同性
XisI-like / XisI protein / XisI-like superfamily / XisI protein / TATA結合タンパク質 / 2-Layer Sandwich / Alpha Beta / XisI protein-like protein
BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
解像度: 1.3→29.099 Å / Num. obs: 52812 / % possible obs: 98.2 % / 冗長度: 3.6 % / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 7.9
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
1.3-1.33
3.6
0.618
1.2
13820
3797
0.618
96.3
1.33-1.37
3.6
0.516
1.4
13539
3742
0.516
97.8
1.37-1.41
3.6
0.419
1.8
13261
3666
0.419
97.7
1.41-1.45
3.6
0.348
2.1
12947
3560
0.348
97.5
1.45-1.5
3.6
0.267
2.8
12569
3468
0.267
97.7
1.5-1.55
3.6
0.222
3.3
12005
3329
0.222
98.1
1.55-1.61
3.6
0.174
4.2
11763
3266
0.174
98.9
1.61-1.68
3.6
0.143
5.1
11286
3140
0.143
98.8
1.68-1.75
3.6
0.117
6.2
10831
3016
0.117
98.9
1.75-1.84
3.6
0.092
7.8
10321
2892
0.092
99.1
1.84-1.94
3.6
0.095
6.6
9863
2772
0.095
99.4
1.94-2.06
3.5
0.062
10.4
9262
2615
0.062
99.5
2.06-2.2
3.5
0.055
11.8
8608
2473
0.055
99.5
2.2-2.37
3.2
0.063
8.5
6824
2137
0.063
93.1
2.37-2.6
3.2
0.046
12.7
6721
2111
0.046
98.9
2.6-2.91
3.5
0.042
14
6758
1912
0.042
99.9
2.91-3.36
3.7
0.037
14.3
6491
1734
0.037
100
3.36-4.11
3.7
0.029
19.8
5129
1394
0.029
97.1
4.11-5.81
3.7
0.026
20.9
4241
1146
0.026
100
5.81-29.1
3.5
0.029
15.1
2252
642
0.029
98.6
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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
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
SOLVE
位相決定
RESOLVE
位相決定
精密化
構造決定の手法: 多波長異常分散 / 解像度: 1.3→29.099 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.699 / SU ML: 0.037 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.056 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 ...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 TO ACCOUNT 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
0.195
2675
5.1 %
RANDOM
Rwork
0.175
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obs
0.176
52745
98.13 %
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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