- PDB-3gyd: Crystal structure of a cyclic nucleotide-binding domain (mfla_192... -
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基本情報
登録情報
データベース: PDB / ID: 3gyd
タイトル
Crystal structure of a cyclic nucleotide-binding domain (mfla_1926) from methylobacillus flagellatus kt at 1.79 A resolution
要素
Cyclic nucleotide-binding domain
キーワード
DNA BINDING PROTEIN / Nucleotide binding protein / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
解像度: 1.79→29.374 Å / Num. obs: 30961 / % possible obs: 99.1 % / 冗長度: 3 % / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 6.144
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
1.79-1.84
2.3
0.559
1.1
4786
2066
0.559
90.8
1.84-1.89
2.7
0.547
1.2
6128
2230
0.547
98
1.89-1.94
3.1
0.473
1.4
6675
2141
0.473
100
1.94-2
3.1
0.366
1.8
6615
2120
0.366
100
2-2.07
3.1
0.271
2.5
6358
2034
0.271
100
2.07-2.14
3.1
0.221
3
6230
2008
0.221
100
2.14-2.22
3.1
0.194
3.5
5947
1896
0.194
100
2.22-2.31
3.1
0.16
4.1
5829
1864
0.16
100
2.31-2.41
3.1
0.132
5
5475
1749
0.132
100
2.41-2.53
3.1
0.126
5.3
5285
1694
0.126
100
2.53-2.67
3.1
0.108
6.3
5099
1626
0.108
100
2.67-2.83
3.1
0.092
7.4
4787
1528
0.092
100
2.83-3.03
3.1
0.083
7.9
4519
1444
0.083
100
3.03-3.27
3.1
0.074
8.6
4173
1342
0.074
99.8
3.27-3.58
3.1
0.066
9.4
3815
1237
0.066
99.9
3.58-4
3.1
0.054
11.1
3531
1135
0.054
99.8
4-4.62
3.1
0.048
13
3050
982
0.048
99.6
4.62-5.66
3.1
0.048
12.9
2603
838
0.048
99.4
5.66-8.01
3
0.056
10.8
1997
659
0.056
98.9
8.01-29.374
2.9
0.041
15.2
1070
368
0.041
96
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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
5.2.0019
精密化
PHENIX
精密化
SHELX
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
MAR345
CCD
データ収集
MOSFLM
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: 1.79→29.374 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 5.717 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.128 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 RECORDS CONTAIN 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 RECORDS CONTAIN 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. AN ADENOSINE-3'-5'-CYCLIC-MONOPHOSPHATE (CMP) IS MODELED INTO THE LIGAND BINDING SITE ON EACH MONOMER BASED ON THE PRESENCE OF CLEAR AND CONCLUSIVE ELECTRON DENSITY.
Rfactor
反射数
%反射
Selection details
Rfree
0.212
1549
5 %
RANDOM
Rwork
0.168
-
-
-
obs
0.17
30921
98.82 %
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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