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.
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実験情報
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実験
実験
手法: X線回折 / 使用した結晶の数: 1
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試料調製
結晶
マシュー密度: 3.12 Å3/Da / 溶媒含有率: 60.57 %
結晶化
温度: 277 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6 詳細: 1.6000M (NH4)2SO4, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
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
0.9792
1
2
0.91837
1
反射
解像度: 2.4→28.892 Å / Num. obs: 21169 / % possible obs: 99.9 % / 冗長度: 4.8 % / Biso Wilson estimate: 49.14 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 7.1
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
2.4-2.46
4.9
0.682
1.1
7338
1512
0.682
100
2.46-2.53
4.8
0.575
1.3
7299
1507
0.575
100
2.53-2.6
4.8
0.481
1.6
7011
1446
0.481
100
2.6-2.68
4.9
0.393
2
6935
1429
0.393
100
2.68-2.77
4.8
0.311
2.4
6628
1370
0.311
100
2.77-2.87
4.8
0.256
3
6495
1342
0.256
100
2.87-2.98
4.8
0.211
3.6
6233
1291
0.211
100
2.98-3.1
4.8
0.159
4.7
5992
1242
0.159
100
3.1-3.24
4.8
0.128
5.8
5697
1184
0.128
100
3.24-3.39
4.8
0.095
7.7
5521
1146
0.095
100
3.39-3.58
4.8
0.078
9
5254
1097
0.078
100
3.58-3.79
4.7
0.072
9.1
4944
1042
0.072
100
3.79-4.06
4.7
0.068
9.5
4663
982
0.068
100
4.06-4.38
4.7
0.062
10.2
4337
918
0.062
100
4.38-4.8
4.7
0.051
12
4024
852
0.051
100
4.8-5.37
4.7
0.046
13.8
3614
769
0.046
100
5.37-6.2
4.6
0.05
13.7
3192
693
0.05
100
6.2-7.59
4.5
0.053
12.3
2678
590
0.053
99.9
7.59-10.73
4.4
0.04
16.3
2097
482
0.04
99.9
10.73-28.89
3.9
0.038
16.6
1076
275
0.038
95.1
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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
データスケーリング
PDB_EXTRACT
3.004
データ抽出
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: 2.4→28.892 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 12.376 / SU ML: 0.148 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.266 / ESU R Free: 0.212 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. FAD IS MODELED BASED ON DENSITY AND STRUCTURAL HOMOLOGY. SO4 IS PRESENT IN CRYSTALLIZATION CONDITION. AN UNKNOWN LIGAND (UNL) WAS MODELLED AT THE PUTATIVE ACTIVE SITE BASED ON A STRUCTURAL HOMOLOG (PDB 2GVC). 5. DENSITY FOR THE FOLLOWING REGIONS ARE POOR: A62,A118,
Rfactor
反射数
%反射
Selection details
Rfree
0.225
1087
5.1 %
RANDOM
Rwork
0.181
-
-
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obs
0.183
21137
99.9 %
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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
原子変位パラメータ
Biso mean: 37.373 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.52 Å2
0 Å2
0 Å2
2-
-
-1.52 Å2
0 Å2
3-
-
-
3.05 Å2
精密化ステップ
サイクル: LAST / 解像度: 2.4→28.892 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
2773
0
84
115
2972
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.014
0.022
2916
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1814
X-RAY DIFFRACTION
r_angle_refined_deg
1.509
1.957
3983
X-RAY DIFFRACTION
r_angle_other_deg
0.934
3
4437
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.82
5
356
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.267
24.741
135
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.121
15
424
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
7.972
15
7
X-RAY DIFFRACTION
r_chiral_restr
0.086
0.2
438
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
3262
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
593
X-RAY DIFFRACTION
r_nbd_refined
0.198
0.2
537
X-RAY DIFFRACTION
r_nbd_other
0.193
0.2
1781
X-RAY DIFFRACTION
r_nbtor_refined
0.186
0.2
1405
X-RAY DIFFRACTION
r_nbtor_other
0.085
0.2
1434
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.211
0.2
138
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.147
0.2
18
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.236
0.2
40
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.204
0.2
8
X-RAY DIFFRACTION
r_mcbond_it
2.085
3
1838
X-RAY DIFFRACTION
r_mcbond_other
0.421
3
726
X-RAY DIFFRACTION
r_mcangle_it
3.351
5
2862
X-RAY DIFFRACTION
r_scbond_it
4.959
8
1287
X-RAY DIFFRACTION
r_scangle_it
6.369
11
1121
LS精密化 シェル
解像度: 2.4→2.462 Å / Total num. of bins used: 20
Rfactor
反射数
%反射
Rfree
0.267
88
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Rwork
0.252
1420
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all
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1508
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obs
-
-
100 %
精密化 TLS
手法: refined / Origin x: 35.2065 Å / Origin y: 28.2679 Å / Origin z: 25.7464 Å