Resolution: 2→42.28 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.927 / SU B: 10.674 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.246
2115
5.1 %
RANDOM
Rwork
0.21
-
-
-
obs
0.212
41788
98.53 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 32.473 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.02 Å2
0 Å2
0 Å2
2-
-
0 Å2
0 Å2
3-
-
-
0.02 Å2
Refinement step
Cycle: LAST / Resolution: 2→42.28 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4442
0
25
301
4768
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.011
0.022
4647
X-RAY DIFFRACTION
r_angle_refined_deg
1.201
1.96
6383
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.604
5
629
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
31.488
23.511
188
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.165
15
658
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
14.504
15
34
X-RAY DIFFRACTION
r_chiral_restr
0.079
0.2
755
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.021
3607
X-RAY DIFFRACTION
r_mcbond_it
0.471
1.5
3085
X-RAY DIFFRACTION
r_mcangle_it
0.796
2
4951
X-RAY DIFFRACTION
r_scbond_it
1.516
3
1562
X-RAY DIFFRACTION
r_scangle_it
2.306
4.5
1420
LS refinement shell
Resolution: 1.999→2.05 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.298
131
-
Rwork
0.238
2777
-
all
-
2908
-
obs
-
-
94.32 %
Refinement TLS params.
Method: 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
1.6819
2.1353
-1.4015
3.9776
0.4043
4.9887
-0.1894
0.1022
0.2003
-0.2635
-0.0096
0.4906
0.213
-0.3538
0.1989
0.1272
-0.02
-0.0502
0.2211
-0.0203
0.1499
27.0511
21.4412
38.9021
2
5.3992
-0.2687
-2.023
0.7868
-2.1288
7.2766
-0.0654
0.4876
-0.49
-0.3727
0.3447
0.2576
1.0125
-1.3328
-0.2793
0.3986
0.0588
-0.2446
0.4904
-0.2008
0.5647
20.3066
25.2352
36.3532
3
9.6978
1.5128
12.9948
3.597
0.3187
19.1011
-0.1624
-0.1397
-0.3511
-0.1999
0.1695
0.0959
0.0819
-0.0202
-0.0071
0.1539
0.0552
0.1357
0.1724
0.1183
0.4008
31.8263
20.7889
37.0216
4
6.5123
1.4984
-2.0439
8.6877
-4.1954
12.3548
-0.0538
0.2782
-0.3238
-0.3011
-0.1531
-0.2615
0.3926
0.2088
0.2069
0.1064
0.0269
0.0028
0.0855
-0.041
0.0368
35.4626
28.981
37.5601
5
6.0575
3.4882
-0.6142
6.694
0.2302
0.1446
0.1389
-0.5114
-0.0354
0.4532
-0.131
0.0579
0.0059
0.0487
-0.0079
0.136
0.0293
0.0435
0.1887
0.0098
0.0851
31.6256
27.2017
51.0458
6
11.1922
-0.5658
-2.2801
2.6748
-0.6707
5.213
0.283
0.5521
-0.1133
-0.1383
-0.2088
0.0154
-0.0445
0.1762
-0.0742
0.1259
-0.0014
-0.0018
0.1097
-0.0377
0.0161
31.4216
36.7164
42.2588
7
4.4132
0.9821
-0.7028
3.5606
-0.8202
1.4757
-0.0983
0.069
-0.5726
-0.089
0.0452
0.229
0.2796
-0.0931
0.0531
0.1409
-0.0101
0.0322
0.177
0.0212
0.2447
18.4363
7.5729
51.3006
8
18.9897
11.427
-5.5122
6.902
-3.2813
1.6614
0.3398
-0.6285
-0.3762
0.2731
-0.3534
-0.2657
-0.0464
0.2514
0.0136
0.2504
-0.0128
-0.0356
0.2958
0.0276
0.2327
19.9143
11.4998
60.0729
9
0.6713
-0.8763
-0.45
2.02
1.009
0.5059
-0.1254
-0.1682
-0.4911
0.3489
0.0024
0.1109
0.1805
-0.0301
0.1231
0.1646
-0.0178
0.063
0.3376
0.2361
0.6909
23.283
5.9198
55.7029
10
4.9682
-1.6834
0.2849
3.8087
-0.208
6.6851
-0.0163
0.7859
-0.6177
-0.7662
-0.2148
-0.2339
0.292
0.0799
0.2311
0.2798
-0.038
0.0543
0.2326
-0.0579
0.365
20.4369
5.4152
44.6768
11
2.0851
1.8198
0.4756
2.2891
-0.3872
1.134
0.2689
-0.2303
0.0554
0.3996
-0.1769
0.2392
-0.1468
-0.1577
-0.092
0.1128
0.023
0.0651
0.1276
-0.0521
0.1953
20.4586
25.4874
51.0064
12
1.0473
-0.6447
-0.6797
1.3727
-0.5892
2.1754
-0.0624
0.1626
0.0731
-0.0145
-0.1089
-0.114
-0.1277
0.102
0.1713
0.1127
-0.0653
-0.0281
0.1106
0.0118
0.1304
32.6574
44.4157
50.0044
13
30.1987
-10.5643
2.3347
24.9314
-1.2584
5.7381
0.2726
-0.7535
-0.4009
1.0694
-0.105
0.1502
-0.345
0.1593
-0.1676
0.1103
-0.0284
-0.0246
0.1036
-0.0096
0.1306
35.3993
48.3368
62.2921
14
1.5155
0.1727
0.1655
10.8158
0.3986
1.7792
-0.0842
0.0245
-0.0262
0.0327
0.1188
0.0193
-0.1016
0.0154
-0.0347
0.068
-0.03
0.0039
0.095
-0.0258
0.0091
28.0008
47.1792
57.624
15
8.3014
-0.9264
-4.9988
11.4731
-3.848
11.9855
-0.3254
0.0543
-1.0045
-0.2197
-0.1205
-0.9878
0.2011
0.8446
0.4459
0.1864
0.0369
0.0399
0.1771
-0.0666
0.2811
41.6029
35.1922
58.897
16
1.0986
-1.2764
0.6859
2.9327
-0.7774
1.6395
-0.0128
0.2123
-0.0337
-0.0336
-0.0386
0.0347
0.0159
0.0554
0.0514
0.0611
-0.0077
0.0103
0.0977
-0.0309
0.0242
28.6657
46.5754
51.2483
17
4.1611
2.4471
1.6065
3.9018
1.1986
2.4304
0.0273
0.1061
-0.0947
0.0904
0.0518
-0.2073
-0.0099
0.2281
-0.0792
0.0814
0.0026
0.0093
0.0753
-0.0008
0.0146
34.4641
47.6158
49.7403
18
3.4762
1.0982
-0.3608
16.3958
2.7425
2.631
0.0881
-0.2354
0.1689
0.5815
-0.3196
0.8007
0.0847
-0.16
0.2315
0.0981
-0.0023
0.0201
0.1499
0.0123
0.0673
16.4362
48.242
53.6611
19
7.2752
8.7615
1.0817
12.7897
-0.1536
1.1133
-0.1293
0.3369
-0.1055
-0.1193
0.0652
-0.2715
-0.0557
0.255
0.0641
0.094
0.0411
0.0167
0.1161
0.0312
0.0387
24.7319
65.2993
51.5503
20
51.5544
20.2748
-23.0572
28.1282
-26.5125
25.4236
0.6825
2.5161
2.3075
-1.1411
-0.9002
-0.4749
0.8548
0.6297
0.2176
0.5232
-0.2324
0.0307
0.82
0.2701
0.2487
32.1879
75.7391
48.9202
21
2.3812
-1.1062
-3.1421
5.0777
-0.8611
5.8822
-0.2206
-0.2245
-0.1538
0.3278
-0.0536
-0.3188
0.2085
0.1889
0.2742
0.1606
0.0053
-0.0306
0.1848
0.0175
0.1095
41.2876
10.7197
67.0815
22
17.8274
8.6746
-8.5397
56.3596
-13.9109
5.9207
-0.3022
-0.8077
-1.5614
1.0869
-0.3759
-0.5972
-0.1138
0.4249
0.6781
0.3684
0.0424
-0.1472
0.6428
0.1654
0.4939
48.2979
13.4095
73.1037
23
7.4879
2.2497
-0.0622
5.7877
-0.1373
6.2877
-0.0389
0.0406
-0.0875
0.2142
-0.0891
0.2136
0.5462
-0.1696
0.128
0.2628
-0.0332
0.0346
0.1501
-0.0263
0.1706
35.2108
9.9763
69.6349
24
23.9258
3.9325
3.742
14.6903
1.0415
17.4809
0.2012
-0.1268
-1.0606
0.2338
0.1494
0.9242
1.0635
-1.109
-0.3505
0.3958
-0.0867
0.0721
0.2329
0.0373
0.2301
30.2288
11.2845
76.5014
25
2.1862
2.1976
-1.9
4.5993
-0.1009
3.0226
-0.0318
-0.1037
-0.0544
-0.0818
-0.0779
0.0111
-0.0281
0.1086
0.1097
0.151
0.0045
-0.0197
0.1695
-0.026
0.1688
36.5485
20.7908
62.8824
26
6.1837
4.7447
13.2972
3.6447
10.1974
28.6036
-0.338
-1.3549
0.5555
-0.2975
-0.9116
0.4716
-0.9625
-2.9859
1.2496
0.3925
0.3951
0.146
0.849
0.1045
0.9259
26.7011
23.4872
72.4921
27
2.692
-4.0793
-4.8834
6.1848
7.4057
8.8713
-0.3443
-0.0301
-0.1753
0.4991
0.0495
0.2491
0.5743
0.076
0.2948
0.2424
0.0249
0.0173
0.168
-0.031
0.1477
45.6257
17.2105
63.5373
28
5.2884
-3.2881
-0.8346
3.6901
1.0564
1.8311
0.2009
0.4044
-0.0425
-0.2237
-0.1621
0.0082
-0.047
-0.0673
-0.0388
0.1277
-0.0181
-0.0071
0.1217
0.0257
0.1044
47.2148
8.844
44.4642
29
9.2365
-2.2447
-5.7835
7.7359
1.8982
16.8116
-0.1369
0.2675
0.3791
-0.3979
0.0879
-0.1461
0.0402
-0.1883
0.049
0.1323
0.0162
0.0403
0.1432
0.084
0.0942
50.9955
16.8273
41.2326
30
5.2423
-0.5736
-1.2585
3.4181
1.7505
4.5626
0.0558
0.0697
-0.4828
0.0781
0.0485
0.2028
0.5242
-0.3136
-0.1043
0.1683
-0.012
0.0187
0.1496
-0.0028
0.1365
42.8043
5.3468
49.4613
31
19.0712
6.8729
6.3895
11.4434
-2.1658
4.3678
-0.025
-0.5853
0.5476
0.7683
-0.1405
0.2431
-0.3935
-0.2349
0.1654
0.3156
0.0377
0.0771
0.2235
0.046
0.1063
50.2068
1.6896
58.5881
32
1.535
-1.7495
-2.0688
2.395
1.9411
3.4783
0.0179
-0.1068
0.1666
0.088
0.107
-0.1467
-0.1684
0.1441
-0.1249
0.0866
-0.0003
-0.0462
0.1638
-0.0147
0.1358
46.1197
18.4976
63.2791
33
4.8909
-1.306
2.3653
3.6783
-0.7652
3.6215
-0.0697
-0.4157
-0.293
0.0805
0.1513
0.1666
0.0786
-0.2391
-0.0816
0.1203
-0.0039
0.0419
0.0849
0.0006
0.0412
32.6645
36.2876
73.3137
34
24.4345
-1.6551
19.9357
5.4374
0.8991
17.2163
-0.0013
0.4973
0.3494
-0.8502
-0.2465
-0.1136
-0.3753
0.3185
0.2479
0.2099
0.003
0.0859
0.131
-0.0669
0.1518
29.1197
45.6111
68.9236
35
0.4812
-1.234
-0.3062
5.7975
4.3832
5.1233
-0.091
0.0041
-0.047
0.2402
0.035
0.1265
0.0963
0.0919
0.0561
0.0789
0.0265
0.0061
0.0824
0.0243
0.1101
37.2956
41.2214
71.8408
36
21.6147
1.0298
1.5531
4.1269
-4.5417
15.4169
-0.046
0.3088
-1.2285
-0.038
0.2313
0.542
0.6384
-0.7952
-0.1853
0.1454
-0.0567
-0.005
0.0831
-0.0129
0.2046
24.8764
33.9269
63.7433
37
1.2437
-0.0982
0.9795
1.407
0.557
1.4193
-0.08
-0.1254
-0.1696
0.1123
0.047
0.0161
0.0424
0.0598
0.033
0.1039
0.0531
0.0181
0.0979
0.0608
0.1127
35.1968
38.6634
78.8379
38
14.7765
-7.4613
-2.1893
5.7693
2.0491
1.281
-0.0703
0.464
-0.2143
0.1265
-0.039
0.2225
0.2495
-0.0526
0.1093
0.1439
0.0171
-0.0005
0.1127
-0.0001
0.0162
34.5138
31.7555
75.5447
39
1.589
-3.6126
-1.8877
13.2195
7.9101
5.6866
0.191
0.0032
0.0118
-0.4918
0.1474
-0.4836
-0.1209
0.3244
-0.3384
0.0778
0.0469
-0.0366
0.1829
-0.0193
0.1235
46.4799
43.5803
80.9969
40
12.7218
-0.8757
-10.2507
2.6737
1.5959
19.0953
-0.0146
-0.6382
-0.3291
0.6883
0.1498
0.076
0.1672
-0.0781
-0.1351
0.1951
0.0524
-0.0069
0.1723
0.0108
0.0695
35.8887
53.6328
95.4764
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
4 - 16
2
X-RAY DIFFRACTION
2
A
17 - 30
3
X-RAY DIFFRACTION
3
A
31 - 36
4
X-RAY DIFFRACTION
4
A
37 - 54
5
X-RAY DIFFRACTION
5
A
55 - 72
6
X-RAY DIFFRACTION
6
A
73 - 83
7
X-RAY DIFFRACTION
7
A
84 - 109
8
X-RAY DIFFRACTION
8
A
110 - 120
9
X-RAY DIFFRACTION
9
A
121 - 138
10
X-RAY DIFFRACTION
10
A
139 - 169
11
X-RAY DIFFRACTION
11
A
170 - 185
12
X-RAY DIFFRACTION
12
A
186 - 212
13
X-RAY DIFFRACTION
13
A
213 - 218
14
X-RAY DIFFRACTION
14
A
219 - 230
15
X-RAY DIFFRACTION
15
A
231 - 242
16
X-RAY DIFFRACTION
16
A
243 - 258
17
X-RAY DIFFRACTION
17
A
259 - 279
18
X-RAY DIFFRACTION
18
A
280 - 290
19
X-RAY DIFFRACTION
19
A
291 - 303
20
X-RAY DIFFRACTION
20
A
304 - 309
21
X-RAY DIFFRACTION
21
B
4 - 20
22
X-RAY DIFFRACTION
22
B
21 - 26
23
X-RAY DIFFRACTION
23
B
27 - 42
24
X-RAY DIFFRACTION
24
B
43 - 50
25
X-RAY DIFFRACTION
25
B
51 - 69
26
X-RAY DIFFRACTION
26
B
70 - 77
27
X-RAY DIFFRACTION
27
B
78 - 94
28
X-RAY DIFFRACTION
28
B
95 - 113
29
X-RAY DIFFRACTION
29
B
114 - 126
30
X-RAY DIFFRACTION
30
B
127 - 156
31
X-RAY DIFFRACTION
31
B
157 - 163
32
X-RAY DIFFRACTION
32
B
164 - 191
33
X-RAY DIFFRACTION
33
B
192 - 210
34
X-RAY DIFFRACTION
34
B
211 - 218
35
X-RAY DIFFRACTION
35
B
219 - 230
36
X-RAY DIFFRACTION
36
B
231 - 244
37
X-RAY DIFFRACTION
37
B
245 - 266
38
X-RAY DIFFRACTION
38
B
267 - 281
39
X-RAY DIFFRACTION
39
B
282 - 297
40
X-RAY DIFFRACTION
40
B
298 - 309
+
About Yorodumi
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