THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL 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: 2.16 Å3/Da / 溶媒含有率: 43.07 %
結晶化
温度: 277 K / pH: 7.5 詳細: 1.4000M Na3Citrate, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
解像度: 1.78→39.621 Å / Num. obs: 15531 / % possible obs: 98.1 % / 冗長度: 2.8 % / Biso Wilson estimate: 21.33 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 9.8
反射 シェル
解像度 (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
% possible all
2-2.05
0.943
2.4
31503
4244
99.9
2.05-2.11
0.788
2.9
30771
4135
100
2.11-2.17
0.638
3.5
29991
4033
100
2.17-2.24
0.516
4.2
29054
3909
100
2.24-2.31
0.469
4.6
28142
3791
100
2.31-2.39
0.402
5.3
27337
3685
100
2.39-2.48
0.338
6.1
26546
3685
100
2.48-2.58
0.304
6.6
25421
3574
100
2.58-2.7
0.236
8.3
24463
3432
100
2.7-2.83
0.215
8.9
23356
3303
100
2.83-2.98
0.166
10.9
22400
3157
100
2.98-3.16
0.132
13.1
21158
3043
100
3.16-3.38
0.11
15.2
19766
2688
100
3.38-3.65
0.092
18.1
18425
2516
100
3.65-4
0.077
21.7
17034
2343
100
4-4.47
0.063
24.8
15489
2147
100
4.47-5.16
0.06
24.6
13543
1894
100
5.16-6.32
0.067
20.7
11606
1650
100
6.32-8.94
0.056
23.8
8895
1300
100
8.94-29.7
0.048
24.7
4719
765
100
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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
5.5.0110
精密化
PHENIX
精密化
SHELX
位相決定
MolProbity
3beta29
モデル構築
SCALA
3.2.25
データスケーリング
PDB_EXTRACT
3.006
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: 1.78→39.62 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.454 / SU ML: 0.099 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.129 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 1,2-ETHANEDIOL (EDO) MOLECULES FROM THE CRYOPROTECTION SOLUTION WERE MODELED INTO THE STRUCTURE.
Rfactor
反射数
%反射
Selection details
Rfree
0.222
788
5.1 %
RANDOM
Rwork
0.177
-
-
-
obs
0.179
15531
97.8 %
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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: 1.4 Å / 溶媒モデル: MASK
原子変位パラメータ
Biso mean: 26.66 Å2
Baniso -1
Baniso -2
Baniso -3
1-
2.57 Å2
0 Å2
0.82 Å2
2-
-
-0.84 Å2
0 Å2
3-
-
-
-1.12 Å2
精密化ステップ
サイクル: LAST / 解像度: 1.78→39.62 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
1321
0
8
141
1470
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.015
0.022
1381
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
943
X-RAY DIFFRACTION
r_angle_refined_deg
1.298
1.964
1875
X-RAY DIFFRACTION
r_angle_other_deg
0.85
3
2311
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.881
5
172
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.624
25.303
66
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.438
15
227
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
22.22
15
6
X-RAY DIFFRACTION
r_chiral_restr
0.08
0.2
201
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.021
1554
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
262
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
1.768
3
859
X-RAY DIFFRACTION
r_mcbond_other
0.485
3
339
X-RAY DIFFRACTION
r_mcangle_it
2.904
5
1387
X-RAY DIFFRACTION
r_scbond_it
5.037
8
522
X-RAY DIFFRACTION
r_scangle_it
7.658
11
488
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS精密化 シェル
解像度: 1.78→1.83 Å / Total num. of bins used: 20
Rfactor
反射数
%反射
Rfree
0.378
47
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Rwork
0.354
1082
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obs
-
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97.58 %
精密化 TLS
手法: refined / Origin x: -4.05 Å / Origin y: 17.88 Å / Origin z: 19.972 Å