#256 - 2021年4月 SARSコロナウイルス2型のスパイクと抗体 (SARS-CoV-2 Spike and Antibodies) 類似性 (1)
#241 - 2020年1月 20年の分子を振り返って (Twenty Years of Molecules) 類似性 (1)
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集合体
登録構造単位
A: Self-alkylating Ribozyme (58-MER) B: Self-alkylating Ribozyme (58-MER) C: Fab HAVx Heavy Chain D: Fab HAVx Light Chain H: Fab HAVx Heavy Chain L: Fab HAVx Light Chain ヘテロ分子
解像度: 1.918→89.85 Å / SU ML: 0.28 / 交差検証法: THROUGHOUT / σ(F): 1.33 / 位相誤差: 26.72 / 立体化学のターゲット値: ML
Rfactor
反射数
%反射
Rfree
0.2271
1994
1.8 %
Rwork
0.1877
-
-
obs
0.1884
110762
97.93 %
溶媒の処理
減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
精密化ステップ
サイクル: LAST / 解像度: 1.918→89.85 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
6738
2474
34
802
10048
拘束条件
Refine-ID
タイプ
Dev ideal
数
X-RAY DIFFRACTION
f_bond_d
0.007
9704
X-RAY DIFFRACTION
f_angle_d
1.036
13746
X-RAY DIFFRACTION
f_dihedral_angle_d
13.283
5592
X-RAY DIFFRACTION
f_chiral_restr
0.055
1631
X-RAY DIFFRACTION
f_plane_restr
0.006
1307
LS精密化 シェル
解像度 (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.918-1.966
0.3773
128
0.3454
7218
X-RAY DIFFRACTION
91
1.966-2.0192
0.3104
139
0.3104
7698
X-RAY DIFFRACTION
98
2.0192-2.0786
0.3266
153
0.2902
7747
X-RAY DIFFRACTION
98
2.0786-2.1457
0.3168
133
0.2707
7781
X-RAY DIFFRACTION
98
2.1457-2.2224
0.3059
145
0.2533
7750
X-RAY DIFFRACTION
98
2.2224-2.3114
0.2575
128
0.2386
7807
X-RAY DIFFRACTION
99
2.3114-2.4166
0.2592
145
0.2283
7793
X-RAY DIFFRACTION
99
2.4166-2.544
0.2965
152
0.2244
7833
X-RAY DIFFRACTION
99
2.544-2.7034
0.2566
147
0.2181
7813
X-RAY DIFFRACTION
99
2.7034-2.9121
0.2641
148
0.2144
7839
X-RAY DIFFRACTION
99
2.9121-3.2052
0.2374
132
0.1934
7817
X-RAY DIFFRACTION
98
3.2052-3.669
0.2103
147
0.1718
7839
X-RAY DIFFRACTION
99
3.669-4.6225
0.1911
149
0.1413
7903
X-RAY DIFFRACTION
99
4.6225-10
0.1625
148
0.1416
7930
X-RAY DIFFRACTION
98
精密化 TLS
手法: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
0.6506
0.0053
-0.2128
0.4952
-0.0641
0.1903
-0.0605
-0.6598
0.1579
0.6011
0.1961
0.1413
-0.3689
-0.0506
-0.1083
0.8588
0.1275
0.0404
0.7264
-0.0373
0.4422
-4.577
16.931
10.177
2
0.4939
0.0307
-0.5316
2.0152
0.4686
0.7467
-0.2574
0.9502
0.1672
-1.4704
0.3961
-0.0218
-0.778
0.1353
-0.0471
1.3146
-0.3217
-0.0818
1.1663
0.1159
0.5124
-34.758
21.376
-53.87
3
0.4591
-0.4442
-0.3742
1.0714
0.4911
1.2343
0.0073
0.0951
-0.0387
-0.1766
0.0498
-0.015
0.0507
0.0116
-0.054
0.2665
-0.0407
-0.0442
0.2144
-0.0033
0.2817
17.87
14.011
-40.175
4
0.9181
0.6018
-0.2506
1.1126
-0.5164
0.7649
-0.0264
-0.0697
0.0054
0.1478
0.0451
-0.0248
-0.0026
-0.0196
-0.0145
0.2666
0.0227
-0.0405
0.1698
-0.0084
0.2717
-55.245
12.196
-3.892
5
1.6935
0.8203
-0.6558
0.8612
-0.3755
0.5507
-0.1227
0.067
-0.3108
-0.1083
0.0297
-0.0654
0.1086
-0.0333
0.1097
0.322
0.0302
-0.0534
0.2058
-0.0054
0.3709
-51.243
-3.654
-10.257
6
0.6812
-0.4669
-0.6188
0.7397
0.3452
0.6203
-0.1044
-0.0402
-0.18
0.0128
0.0499
0.0762
0.1106
0.0752
0.0617
0.3375
-0.0447
-0.0656
0.2712
-0.0042
0.3325
15.108
-2.884
-35.996
7
0.369
0.0012
-0.0567
0.0083
-0.0212
0.0473
-0.0067
-0.0001
-0.073
-0.0106
0.0015
0.0208
0.0138
-0.0065
0.0083
0.3927
-0.0013
-0.0366
0.3022
-0.0016
0.3813
-18.015
9.832
-21.297
精密化 TLSグループ
ID
Refine-ID
Refine TLS-ID
Selection details
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
( CHAINAAND ( RESID1:58ORRESID101:101 ) )
A
1 - 58
2
X-RAY DIFFRACTION
1
( CHAINAAND ( RESID1:58ORRESID101:101 ) )
A
101
3
X-RAY DIFFRACTION
2
( CHAINBAND ( RESID1:58ORRESID101:101 ) )
B
1 - 58
4
X-RAY DIFFRACTION
2
( CHAINBAND ( RESID1:58ORRESID101:101 ) )
B
101
5
X-RAY DIFFRACTION
3
( CHAINHANDRESID3:230 )
H
3 - 230
6
X-RAY DIFFRACTION
4
( CHAINCANDRESID3:229 )
C
3 - 229
7
X-RAY DIFFRACTION
5
( CHAINDANDRESID1:214 )
D
1 - 214
8
X-RAY DIFFRACTION
6
( CHAINLANDRESID1:214 )
L
1 - 214
9
X-RAY DIFFRACTION
7
( CHAINAANDRESID201:285 ) OR ( CHAINBANDRESID201:236 ) OR ( CHAINCANDRESID301:479 ) OR ( CHAINDANDRESID301:445 ) OR ( CHAINHANDRESID301:494 ) OR ( CHAINLANDRESID