- PDB-2oqm: Crystal structure of a dinb family member protein (sden_0562) fro... -
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基本情報
登録情報
データベース: PDB / ID: 2oqm
タイトル
Crystal structure of a dinb family member protein (sden_0562) from shewanella denitrificans at 1.83 A resolution
要素
Hypothetical protein
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 DUF1993 / Domain of unknown function (DUF1993) / dinb family like domain / DinB/YfiT-like putative metalloenzymes / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / FORMIC ACID / Uncharacterized protein
モノクロメーター: Single crystal Si(111) bent (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
0.97908
1
3
0.97874
1
反射
解像度: 1.83→45.22 Å / Num. obs: 68483 / % possible obs: 92.9 % / Biso Wilson estimate: 31.626 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 8.61
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 all
% possible all
1.83-1.9
0.467
2.2
14330
6155
83.2
1.9-1.97
0.373
2.7
12889
5521
87.3
1.97-2.06
0.282
3.5
14599
6244
89.5
2.06-2.17
0.211
4.6
15071
6474
92.1
2.17-2.31
0.157
5.9
15764
6766
94.8
2.31-2.48
0.122
7.2
14791
6323
95.7
2.48-2.73
0.088
9.2
15790
6770
96.9
2.73-3.13
0.066
12.1
16052
6869
97
3.13
0.042
16.7
15867
6753
97.6
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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
SHELX
位相決定
REFMAC
5.2.0019
精密化
XSCALE
データスケーリング
PDB_EXTRACT
2
データ抽出
MAR345
CCD
データ収集
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: 1.83→45.22 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.956 / SU B: 6.306 / SU ML: 0.093 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.115 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 RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...詳細: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. 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. 4. FMT, CL AND EDO ARE MODELED BASED ON THE CRYSTALLIZATION CONDITIONS OR CRYOPROTECTANT. 5. THE REGION D115-123 HAS POORLY DEFINED ELECTRON DENSITY.
Rfactor
反射数
%反射
Selection details
Rfree
0.196
3437
5 %
RANDOM
Rwork
0.157
-
-
-
all
0.159
-
-
-
obs
0.159
68463
98.4 %
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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