SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "AE" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -7-STRANDED BARREL THIS IS REPRESENTED BY A -6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -3-STRANDED BARREL THIS IS REPRESENTED BY A -2-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -1-STRANDED BARREL THIS IS REPRESENTED BY A 0-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -2-STRANDED BARREL THIS IS REPRESENTED BY A -1-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CE" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 0-STRANDED BARREL THIS IS REPRESENTED BY A 1-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DF" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -3-STRANDED BARREL THIS IS REPRESENTED BY A -2-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.
プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長
波長: 1 Å / 相対比: 1
反射
解像度: 3.03→50 Å / Num. obs: 139069 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / 冗長度: 8 % / Biso Wilson estimate: 84.94 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 14.37
反射 シェル
解像度: 3.03→3.21 Å / 冗長度: 7.8 % / Rmerge(I) obs: 1.27 / Mean I/σ(I) obs: 2 / % possible all: 99.8
-
解析
ソフトウェア
名称
バージョン
分類
PHENIX
(PHENIX.REFINE: 1.8_1069)
精密化
XDS
データ削減
XSCALE
データスケーリング
CNS
位相決定
精密化
構造決定の手法: 単波長異常分散 開始モデル: NONE 解像度: 3.03→19.975 Å / SU ML: 0.36 / σ(F): 0.75 / 位相誤差: 24.29 / 立体化学のターゲット値: ML 詳細: A FOBS OVER SIGMA_FOBS CUTOFF OF 0.75 WAS APPLIED OWING TO ANISOTROPY OF THE DATA. THE MODEL WAS REFINED AGAINST ANOMALOUSLY SCALED DATA
Rfactor
反射数
%反射
Rfree
0.2221
5159
4.2 %
Rwork
0.1899
-
-
obs
0.1913
123933
89.08 %
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
原子変位パラメータ
Biso mean: 147.9 Å2
Baniso -1
Baniso -2
Baniso -3
1-
8.7713 Å2
0 Å2
0 Å2
2-
-
8.7713 Å2
0 Å2
3-
-
-
-17.5426 Å2
精密化ステップ
サイクル: LAST / 解像度: 3.03→19.975 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
14274
0
342
12
14628
拘束条件
Refine-ID
タイプ
Dev ideal
数
X-RAY DIFFRACTION
f_bond_d
0.004
14820
X-RAY DIFFRACTION
f_angle_d
0.978
20033
X-RAY DIFFRACTION
f_dihedral_angle_d
15.129
5665
X-RAY DIFFRACTION
f_chiral_restr
0.065
2421
X-RAY DIFFRACTION
f_plane_restr
0.004
2451
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 (%)
3.03-3.0643
0.3563
141
0.342
3320
X-RAY DIFFRACTION
74
3.0643-3.1002
0.3683
147
0.3354
3338
X-RAY DIFFRACTION
75
3.1002-3.1379
0.3451
133
0.3092
3291
X-RAY DIFFRACTION
74
3.1379-3.1775
0.3132
148
0.2979
3373
X-RAY DIFFRACTION
76
3.1775-3.2191
0.311
165
0.2765
3552
X-RAY DIFFRACTION
80
3.2191-3.263
0.3117
150
0.2706
3647
X-RAY DIFFRACTION
80
3.263-3.3094
0.335
151
0.2619
3535
X-RAY DIFFRACTION
82
3.3094-3.3586
0.2757
161
0.2517
3655
X-RAY DIFFRACTION
82
3.3586-3.4108
0.295
153
0.2479
3649
X-RAY DIFFRACTION
81
3.4108-3.4665
0.2764
166
0.2423
3845
X-RAY DIFFRACTION
87
3.4665-3.5259
0.2795
157
0.236
3666
X-RAY DIFFRACTION
82
3.5259-3.5897
0.2758
173
0.2199
3788
X-RAY DIFFRACTION
85
3.5897-3.6583
0.2512
154
0.2058
3839
X-RAY DIFFRACTION
86
3.6583-3.7325
0.2706
169
0.1981
3998
X-RAY DIFFRACTION
90
3.7325-3.8131
0.2455
176
0.1874
4011
X-RAY DIFFRACTION
91
3.8131-3.9012
0.1833
159
0.1897
4066
X-RAY DIFFRACTION
91
3.9012-3.998
0.2426
188
0.1782
4011
X-RAY DIFFRACTION
90
3.998-4.1052
0.2181
191
0.1703
4139
X-RAY DIFFRACTION
93
4.1052-4.2249
0.1709
186
0.161
4173
X-RAY DIFFRACTION
94
4.2249-4.3599
0.1739
184
0.1449
4270
X-RAY DIFFRACTION
96
4.3599-4.514
0.1862
191
0.1442
4203
X-RAY DIFFRACTION
96
4.514-4.6925
0.176
191
0.1398
4325
X-RAY DIFFRACTION
97
4.6925-4.9031
0.1763
194
0.1451
4419
X-RAY DIFFRACTION
98
4.9031-5.1573
0.1836
189
0.1517
4324
X-RAY DIFFRACTION
98
5.1573-5.4742
0.236
188
0.1692
4397
X-RAY DIFFRACTION
98
5.4742-5.8868
0.1984
191
0.1831
4387
X-RAY DIFFRACTION
98
5.8868-6.461
0.2607
193
0.2019
4376
X-RAY DIFFRACTION
99
6.461-7.3547
0.2549
199
0.2036
4453
X-RAY DIFFRACTION
100
7.3547-9.1172
0.1594
190
0.1711
4423
X-RAY DIFFRACTION
100
9.1172-19.9756
0.2069
181
0.1924
4301
X-RAY DIFFRACTION
97
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
3.8796
-0.2813
-0.2002
5.0183
1.515
3.3983
-0.192
-0.6452
0.1
0.388
-0.0054
0.4552
0.196
-0.7833
0.154
0.519
-0.0693
0.0301
1.3032
-0.0119
0.5424
28.7681
-37.4572
-50.6364
2
3.4672
-0.9047
0.9709
4.2468
-1.6593
2.9042
-0.1651
0.0828
0.2112
0.0809
0.3308
0.2848
-0.5511
-0.5126
-0.0846
1.0046
0.4316
-0.0166
0.7579
0.0195
0.6171
44.2293
-13.3694
-9.5726
3
4.0108
0.2292
-1.4998
1.9852
-1.0611
4.5453
-0.0133
0.4847
-0.0774
-0.4044
0.0508
0.0415
0.2349
-0.2925
-0.042
0.6416
0.0825
-0.0714
0.4881
-0.0099
0.3409
69.0417
-50.0313
24.0861
4
1.7036
-0.7893
-0.1033
5.202
-1.5361
1.7173
-0.2004
0.0817
0.4449
0.0999
0.4692
0.9785
-0.8048
-0.6028
-0.2612
2.0707
0.8461
-0.0568
1.224
-0.081
1.2686
31.0649
15.7481
-17.7785
5
5.1989
-0.5434
-1.1206
4.8061
3.1708
3.7765
-0.5062
-2.6862
0.6194
1.2427
0.0946
-0.8549
0.3942
-2.124
0.0929
1.144
0.462
-0.1816
3.247
-0.5991
0.6859
18.7342
-25.2079
-27.5867
6
4.9026
0.4302
-0.1888
4.1746
-0.8226
3.5646
-0.1611
-0.4578
-0.0406
0.2155
0.1114
0.1133
-0.5626
-0.1925
0.1152
0.8128
0.2697
-0.0391
0.5554
0.0037
0.3716
58.759
-27.4899
8.5088
7
6.6653
-1.2518
0.9206
4.9507
1.7991
8.3883
0.1875
0.3481
0.3429
-0.627
-0.0334
-0.5826
-0.3216
1.1783
-0.1689
0.532
-0.0161
0.0961
0.6714
0.0504
0.481
92.7078
-46.2693
11.8633
8
4.1344
-2.6444
0.0742
3.2055
1.1934
0.896
-0.323
-0.1364
0.6171
-0.4612
0.284
-0.1539
-1.3665
-0.0405
0.1016
2.8651
0.6632
-0.1413
1.1429
0.0639
1.5757
39.7284
32.1057
-35.8225
9
7.1631
-1.7293
0.4277
4.1516
0.6407
0.847
-0.4604
-0.6793
0.2115
-0.8553
-0.3022
0.3052
0.2225
-1.6377
0.4152
0.7311
0.3386
-0.1831
3.1547
-0.5029
1.176
0.6591
-28.2522
-51.7151
10
6.6356
1.0845
-2.6046
5.8482
0.5514
4.2903
0.4148
0.3358
-0.2679
-1.1137
0.1331
1.523
0.0781
-2.2404
-0.4529
1.0664
0.0479
-0.3082
1.5665
0.2928
0.9417
30.3508
-37.2433
1.6851
11
2.371
-0.0758
-1.0561
1.8612
-1.8721
3.8413
0.0248
-0.3913
-0.05
0.2541
-0.2725
-0.3115
-0.3889
0.5108
0.1569
0.5838
0.0408
-0.0617
0.8932
0.0007
0.4739
94.4614
-53.3596
41.8886
12
7.4185
3.9042
1.8357
5.504
2.0599
0.5966
-0.2949
-0.7185
0.9401
-0.0803
0.0207
-1.3277
-0.8976
0.3085
0.1668
2.1598
0.0117
-0.3137
0.9508
-0.1629
1.4605
61.9521
14.9965
-25.1015
13
8.3217
-0.2954
7.4167
3.9303
-0.1234
7.3655
-0.3292
-1.5243
0.7535
0.6426
0.143
-0.7028
-0.8286
0.4455
0.2244
0.9143
0.0208
-0.1473
2.4283
-0.2574
1.2618
-24.7104
-22.5441
-76.2041
14
2.5783
3.574
-1.9966
4.6593
-1.4888
7.0662
-0.0269
1.14
1.8406
-0.458
0.0228
1.9032
0.6544
-2.3321
0.1577
1.5731
-0.1712
-0.2483
2.136
0.2997
2.3188
-1.542
-50.0663
-1.1349
15
7.7184
0.2912
4.8244
8.1571
-1.6315
5.9554
-0.0826
-0.9767
-0.2476
1.0379
-0.0736
-1.4164
0.1307
1.4608
0.1457
0.9044
0.1
-0.2093
1.5361
0.02
0.8929
111.373
-55.2441
74.0806
16
0.1178
0.302
-0.5033
2.3139
-2.9411
1.1042
0.3642
-0.5709
0.4397
0.0099
-0.6811
-1.3285
-0.2436
0.4413
0.0394
2.5478
-0.4189
-0.0484
2.0333
-0.1645
3.1037
96.3593
7.12
-15.996
17
2.0029
4.657
3.7135
2.0041
-0.4256
0.9385
0.0848
-1.0074
0.4324
1.3039
-0.1942
-1.2052
-0.9127
2.6129
0.1349
2.1267
0.1294
-1.3938
2.0187
-0.4611
3.4513
29.9422
-21.8543
-14.5523
18
6.5126
8.3778
5.2592
2.0008
2.7216
2.0043
-0.4631
-0.1149
0.5797
-0.0406
0.4842
0.1651
0.0809
0.6054
0.0196
1.4931
-0.239
-0.7348
0.8126
0.5444
1.6008
75.3035
-24.8428
4.7275
19
4.066
-8.5854
-1.1598
2.0165
4.4779
2.0073
0.9879
-1.2144
-1.1265
0.7938
-0.8789
1.0858
1.1299
-1.0308
-0.1621
0.9896
-0.1872
0.1185
0.6664
0.1441
0.7553
70.159
-61.8383
40.5836
20
2.0026
4.1686
-3.2416
2.0081
2.0054
2.0056
-0.5908
0.6748
-0.7982
-0.3939
0.6446
0.3116
1.4515
-1.3994
0.0918
0.9126
-0.1703
-0.3716
1.0723
-0.0697
0.7657
48.6559
-56.8323
27.2072
21
2.0004
8.4158
-2.6674
2.0085
8.6963
2.0035
-0.3732
0.7878
0.5848
-1.0649
0.0134
0.7493
-1.2752
-1.5998
0.2498
0.8223
-0.1897
0.0585
1.0458
-0.0885
0.4874
49.3218
-49.7956
30.5379
22
2.0017
2.3729
1.9908
2.0281
-6.3821
2.0205
0.2458
-0.2885
-1.2136
0.1734
-0.1864
-0.4173
0.3729
-0.1828
0.0045
1.2334
0.1048
0.0106
0.4993
0.0169
0.4638
79.6854
-58.5185
53.7107
23
2.0006
2
2
2.0005
2.0002
2.0007
10.3569
-15.128
7.2376
24.8059
-6.9873
-15.6737
-2.9841
-51.4276
-3.364
2.5081
-0.373
0.0464
2.6565
-0.2811
1.0834
49.2787
-36.0757
-10.6148
24
2.0002
1.9993
2.0002
2.0012
1.9997
2.001
3.2757
-60.6123
-12.7486
4.3671
4.4926
47.438
-3.3289
-21.8593
-7.8205
1.1282
0.0393
0.3008
2.9423
0.7474
2.8915
72.9833
-38.1422
4.9523
25
1.9998
1.9998
-5.1924
2
2
2.0001
-2.6967
-1.7744
3.5473
1.3419
1.6392
5.9416
-6.4295
-18.32
1.0458
1.5119
-0.0056
-1.0029
1.7691
0.3382
1.1259
79.7227
-49.2523
43.6793
26
2.0002
2.0002
2.0002
2.0001
2.0002
2.0003
-1.2685
15.8423
5.7909
37.4231
6.4348
-12.2732
6.8807
0.4892
-5.1871
1.6926
0.2063
-0.5013
1.3802
0.3199
0.8212
75.877
-45.1232
47.0393
27
2.0009
2.0004
2.0001
2.0002
2
2.0003
-3.4712
-5.4785
-11.0228
8.0551
2.3548
-47.855
17.889
-22.0573
1.1231
1.005
0.1274
0.0011
1.7471
-0.3578
1.9929
113.3473
-54.7235
57.6637
28
2.0004
2
2.0003
2.0004
1.9999
2.0003
20.4306
27.2398
-6.5571
-10.2299
-10.9256
3.6906
26.1641
24.226
-9.498
2.0079
0.4516
-0.5192
2.2203
1.2342
1.7556
72.6322
-66.889
32.7758
29
2.0003
2
-5.0768
2.0003
1.9998
2.0003
3.7649
12.1187
-14.2884
-14.176
-6.114
5.1808
-26.5585
9.7408
2.3511
1.4188
0.6585
-0.0023
1.6678
0.4541
1.2722
90.3702
-65.734
54.394
精密化 TLSグループ
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
((CHAINAANDRESID0:179) OR (CHAINAANDRESID1469:1470) OR (CHAINAANDRESID2001:2004))
2
X-RAY DIFFRACTION
2
((CHAINBANDRESID1:179) OR (CHAINBANDRESID1469:1470) OR (CHAINBANDRESID2001:2004))
3
X-RAY DIFFRACTION
3
((CHAIN C AND RESID -2:179) OR (CHAIN C AND RESID 1469:1470) OR (CHAIN C AND RESID 2001:2004))