A: uncharacterized protein B: uncharacterized protein C: uncharacterized protein D: uncharacterized protein E: uncharacterized protein F: uncharacterized protein G: uncharacterized protein H: uncharacterized protein hetero molecules
Resolution: 2.8→2.85 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.808 / Mean I/σ(I) obs: 1.69 / % possible all: 100
-
Processing
Software
Name
Version
Classification
NB
REFMAC
5.6.0117
refinement
PDB_EXTRACT
3.1
dataextraction
SBC-Collect
datacollection
HKL-3000
datareduction
HKL-3000
datascaling
HKL-3000
phasing
MLPHARE
phasing
DM
phasing
SHELXDE
phasing
ARP/wARP
modelbuilding
RESOLVE
phasing
Coot
modelbuilding
Refinement
Method to determine structure: SAD / Resolution: 2.82→91.75 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 32.045 / SU ML: 0.264 / Cross valid method: THROUGHOUT / ESU R Free: 0.337 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.25154
2272
5.1 %
RANDOM
Rwork
0.17693
-
-
-
obs
0.18063
42712
98.77 %
-
all
-
44984
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 77.149 Å2
Baniso -1
Baniso -2
Baniso -3
1-
4.42 Å2
0 Å2
3.91 Å2
2-
-
-5.79 Å2
0 Å2
3-
-
-
6.59 Å2
Refinement step
Cycle: LAST / Resolution: 2.82→91.75 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
9179
0
10
57
9246
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.006
0.019
9224
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.012
1.961
12447
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.35
5
1158
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
45.364
26.719
512
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
17.114
15
1828
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
14.716
15
80
X-RAY DIFFRACTION
r_chiral_restr
0.064
0.2
1467
X-RAY DIFFRACTION
r_gen_planes_refined
0.003
0.021
6932
X-RAY DIFFRACTION
r_gen_planes_other
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
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
X-RAY DIFFRACTION
r_scbond_it
X-RAY DIFFRACTION
r_scangle_it
X-RAY DIFFRACTION
r_rigid_bond_restr
4.25
3
9224
X-RAY DIFFRACTION
r_sphericity_free
31.297
5
32
X-RAY DIFFRACTION
r_sphericity_bonded
20.46
5
9214
LS refinement shell
Resolution: 2.817→2.89 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.353
141
-
Rwork
0.293
2712
-
obs
-
-
87.03 %
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
0.7402
0.2668
-0.8625
2.6342
-2.0213
2.1737
-0.0099
0.0721
-0.1406
0.2802
-0.1101
-0.0471
-0.1957
0.0295
0.12
0.2108
-0.0162
-0.0524
0.2232
-0.0721
0.1643
-20.0358
120.9109
-1.5911
2
15.4529
-20.809
-3.0711
28.2477
4.0481
0.6465
-0.1678
0.071
-0.6154
0.143
0.0658
0.8843
0.0888
-0.0663
0.1019
0.2487
0.004
-0.0894
0.2539
-0.0483
0.156
-20.4153
143.1852
-18.4263
3
5.1341
-2.2565
2.0943
19.6025
-1.8872
1.3135
0.2921
0.3891
-0.0472
-0.8153
-0.0497
0.6755
-0.0812
0.2776
-0.2424
0.1888
-0.0404
0.079
0.2305
-0.0032
0.1348
-33.93
169.4357
-14.8874
4
12.3818
-14.2187
2.5442
22.4756
-0.5977
1.4092
-0.5107
-0.9123
-0.6204
0.8543
0.8771
0.234
-0.0012
-0.2281
-0.3664
0.2795
-0.0664
0.1051
0.1619
-0.0186
0.2487
-28.6272
171.6309
-7.1231
5
8.7468
-11.914
-5.5025
18.739
6.7842
3.6639
-0.2673
-0.4015
0.3746
0.5652
0.4115
-0.8655
0.0998
0.2905
-0.1441
0.2019
-0.0573
-0.1018
0.1524
-0.0119
0.248
-13.1399
146.2241
-12.3692
6
1.0761
-0.0734
-1.98
1.1192
-0.5341
4.0461
-0.0524
-0.1038
-0.0496
0.06
-0.0355
-0.0031
0.0703
0.2305
0.0879
0.1425
0.0292
-0.008
0.2455
-0.0136
0.224
-15.9716
121.0912
-2.7159
7
6.6336
-2.271
2.9531
0.8225
-0.9677
1.6334
-0.0526
0.2642
-0.1258
0.0349
-0.0621
0.1253
0.0693
0.1417
0.1147
0.1735
0.0122
-0.0039
0.2056
0.0016
0.2172
-35.2322
118.3042
-13.7867
8
3.959
9.7716
4.9442
52.5247
14.5868
6.3814
0.3636
-0.2053
-0.0625
1.3165
-0.3586
0.3539
0.4736
-0.2616
-0.005
0.0951
-0.0017
-0.0071
0.2266
0.0348
0.1771
-54.0251
138.1156
-17.7812
9
14.2368
5.0392
5.7949
26.0787
11.1212
5.9276
-2.2088
-0.6982
0.2859
1.4589
1.0386
3.7376
0.0805
0.3868
1.1702
0.7083
0.2083
0.1554
0.3983
-0.0203
0.8217
-50.2595
165.6572
-6.0105
10
4.9683
9.0179
4.3352
19.7346
11.7575
8.2831
0.3456
-0.5297
-0.0443
0.5147
-0.5198
0.1194
0.1895
0.0426
0.1742
0.1037
-0.0979
0.0329
0.2667
-0.0649
0.1982
-41.5606
166.0761
-9.0301
11
5.3206
9.2547
8.0805
32.8693
17.6665
15.1434
-0.0816
0.3353
-0.2074
-0.7181
0.841
-0.9596
-0.2702
0.7352
-0.7594
0.0518
-0.0232
-0.0031
0.1751
0.0175
0.1948
-46.659
139.9346
-23.7062
12
0.3669
0.1154
0.0271
0.7198
0.1776
0.05
-0.0222
0.108
-0.0618
0.1378
-0.021
0.1516
0.057
0.0218
0.0432
0.1872
-0.0066
0.0051
0.2955
0.0092
0.1944
-40.1473
117.8879
-10.5569
13
5.2685
14.2421
-0.7476
45.2071
-2.0609
0.1104
0.4517
0.211
-0.2588
3.0022
-0.4705
-0.3904
-0.102
-0.052
0.0188
0.6697
-0.0728
0.1118
0.3606
-0.0009
0.0439
-52.8239
140.414
19.7669
14
9.9626
14.1511
-1.1614
33.8361
-3.748
3.2092
0.4483
0.0232
-0.5119
1.1183
-0.3787
-0.4765
-0.139
0.3798
-0.0696
0.1102
-0.0524
-0.0556
0.1888
0.01
0.0583
-42.3689
167.7081
16.0444
15
6.1234
12.8435
-5.6046
30.1947
-11.7127
5.4138
-0.2609
-0.0185
-0.4123
-0.6523
-0.0172
-0.4636
0.0467
0.3378
0.2781
0.2151
-0.2052
0.0397
0.3782
-0.0971
0.1276
-43.9397
167.2916
6.4989
16
9.9005
10.2152
-3.9108
24.2231
-3.0634
1.6177
-0.6223
0.8589
-0.4653
-0.4769
0.3785
0.3974
0.2352
-0.3654
0.2438
0.2506
-0.0305
0.1172
0.2303
-0.0354
0.1735
-58.2489
141.1858
11.5602
17
1.601
0.272
-2.5781
0.1562
-0.4355
4.2343
0.0536
0.1459
0.0252
0.0752
-0.0519
0.1753
0.03
-0.1849
-0.0017
0.2129
-0.0322
0.1241
0.2191
-0.0589
0.2952
-51.1824
117.7002
2.792
18
3.5846
2.9666
3.5066
3.2924
2.5152
3.7318
-0.1283
-0.0585
-0.0848
0.2025
-0.0269
-0.2148
-0.1474
-0.1174
0.1552
0.2794
0.0108
0.1322
0.1746
-0.0244
0.2766
-31.6123
120.1529
14.0161
19
1.2561
-5.5944
1.7643
25.4583
-7.924
6.0756
0.1945
0.1187
0.1409
-1.2361
-0.3041
-0.6499
0.2896
0.173
0.1096
0.2791
-0.1247
-0.0366
0.1358
-0.0126
0.2299
-15.1973
144.7333
19.2014
20
6.6595
-9.3191
0.703
47.1681
-13.2937
4.5181
0.6808
0.5709
0.6266
-0.9901
-1.1965
-2.132
0.1168
0.2273
0.5157
0.3119
0.1529
-0.0488
0.1795
-0.0136
0.1744
-19.8459
173.1726
10.6771
21
1.1169
1.0484
-1.4486
7.2046
1.0521
2.8852
-0.1234
0.5296
0.1227
-0.9341
0.286
0.3571
-0.0432
-0.8039
-0.1626
0.282
-0.0372
-0.2136
0.3207
0.0425
0.3026
-28.4654
172.6249
13.5521
22
1.3413
-6.7122
2.1992
33.9119
-10.5277
5.5195
-0.1323
-0.2568
-0.2296
0.473
1.0548
1.151
-0.0117
-0.7847
-0.9226
0.2554
0.002
-0.0767
0.2908
-0.0068
0.3266
-22.9612
145.3344
25.1117
23
5.0119
0.8399
3.0041
1.6874
-0.0203
1.9851
0.0883
-0.1382
-0.115
0.2985
-0.0526
-0.0929
-0.0477
-0.1059
-0.0356
0.2687
0.0214
0.0851
0.1859
0.0013
0.0949
-30.8549
119.7815
17.7481
24
2.95
0.4773
4.2498
1.8042
1.7589
6.8114
0.04
0.0387
0.1145
-0.0824
-0.2192
0.0124
0.0428
-0.014
0.1792
0.1264
0.0296
0.0474
0.3263
0.0419
0.1083
-10.3709
188.7249
41.5918
25
11.8019
-21.0758
3.3585
51.55
-5.9661
2.0221
0.0636
-0.3147
0.2728
-2.1036
0.1166
-1.1917
-0.0201
-0.1105
-0.1802
0.2924
0.024
0.1176
0.2068
-0.0156
0.1089
-14.7261
168.2581
21.8184
26
6.4842
-13.5711
-1.5416
29.4039
5.3963
5.6279
0.6796
-0.04
0.2199
-1.306
-0.0667
-0.6134
0.6431
-0.435
-0.613
0.4913
-0.1532
-0.1354
0.0925
0.0725
0.2696
-3.1748
140.55
23.4423
27
18.2752
-18.7422
7.4436
20.061
-7.2206
3.2367
-0.6367
-1.3382
-0.5698
-0.3645
1.2548
0.0278
-0.6632
-0.5648
-0.6182
1.0573
0.0075
0.5496
0.1696
0.1547
0.5271
-6.4468
139.2589
32.5155
28
8.3249
-13.118
2.425
33.303
-3.5319
0.7159
-0.4271
-0.7776
-0.0836
1.3528
0.4397
0.4043
-0.0991
-0.265
-0.0126
0.2143
-0.067
-0.0352
0.2634
-0.0481
0.0583
-20.7166
166.2894
29.1329
29
1.3381
-0.3862
2.1762
0.4904
0.1238
5.0523
0.029
-0.0543
-0.1053
-0.0767
-0.0411
0.1085
-0.0868
-0.1452
0.0121
0.1919
0.034
-0.0117
0.206
-0.0039
0.1729
-14.2672
188.8043
40.6236
30
12.8327
-4.4367
-8.457
1.5551
3.0418
6.5891
0.3469
0.1983
0.6501
-0.1585
-0.1019
-0.2407
-0.2823
-0.3409
-0.2451
0.221
-0.0162
0.1347
0.178
0.0091
0.281
5.5586
189.5224
30.0065
31
2.8173
3.1126
-0.2926
45.4652
-8.7681
1.9231
-0.0503
-0.1166
0.0017
1.2692
0.3155
-0.2729
-0.2667
-0.0967
-0.2652
0.0828
-0.0045
0.0166
0.2387
-0.0053
0.4852
23.945
167.8773
23.0458
32
0.8165
3.1424
-2.668
13.7589
-11.2687
9.3657
-0.0419
-0.0989
-0.0211
0.6556
-0.2317
-0.6308
-0.4155
0.1715
0.2736
0.3874
0.0771
-0.1301
0.1688
0.0238
0.4333
18.3257
139.6155
31.4614
33
1.4693
5.2693
-2.8529
29.5954
-9.1775
5.6575
0.1114
0.0183
0.3157
1.2961
0.5845
0.6356
-0.1124
-0.0247
-0.6959
0.1345
0.03
-0.0262
0.2009
0.0674
0.2043
9.0029
140.8456
29.993
34
2.4291
7.047
-2.7737
25.2497
-7.7169
3.2058
0.0882
0.0628
0.2655
-0.4806
0.2075
1.0814
-0.1131
-0.1053
-0.2957
0.1941
-0.0583
-0.0181
0.2494
-0.006
0.241
16.4622
167.5414
17.1033
35
4.4242
-0.226
-2.665
0.1711
0.0833
1.6366
0.0766
0.0648
0.1887
-0.1733
-0.0335
-0.1497
-0.0133
-0.0676
-0.0431
0.2352
0.052
0.0957
0.2092
-0.0084
0.1905
6.4157
190.0768
26.2818
36
4.3125
-2.5042
4.5359
1.5857
-2.442
5.1659
0.1045
0.1622
0.138
0.0068
-0.0815
-0.2333
0.0913
0.0893
-0.023
0.2111
0.0279
-0.062
0.1811
-0.0912
0.3142
18.3724
185.0313
47.6932
37
7.4041
14.0685
4.0574
38.1879
9.1756
2.5354
-0.3081
-0.1619
0.2053
1.1221
0.3102
1.3349
0.0978
0.0439
-0.0021
0.2965
0.0513
0.0528
0.2195
-0.0332
0.4615
22.4184
161.7311
61.2109
38
5.3395
11.172
2.9083
31.6281
5.9973
1.6307
0.2348
-0.2528
0.4329
1.1764
-0.3957
0.61
0.1971
-0.1286
0.1609
0.2316
-0.0215
-0.0258
0.1903
-0.0295
0.3263
12.7518
133.8931
55.8005
39
1.4189
5.2632
1.0384
26.3792
5.9864
2.6824
-0.3003
0.1581
0.3444
-0.516
0.2212
0.9326
-0.0751
-0.2803
0.079
0.1725
-0.0351
-0.0734
0.1841
-0.0113
0.2639
15.3688
134.2869
47.0986
40
10.7245
14.8625
5.3437
29.4061
8.2991
2.7562
-0.5335
0.2537
0.157
-1.0919
0.4817
0.2028
-0.2955
0.1361
0.0518
0.1521
-0.0025
-0.005
0.2507
-0.0213
0.1568
28.1223
161.226
53.469
41
1.4701
-0.7229
2.687
0.6539
-1.3333
4.9399
-0.089
0.1218
0.0559
0.0393
-0.0191
-0.3139
-0.1419
0.1617
0.1081
0.123
-0.0034
-0.0076
0.1696
-0.0533
0.3213
21.0719
187.0358
46.3902
42
9.3748
4.4496
-6.0216
2.201
-2.7341
4.576
0.0832
-0.3269
0.4175
0.1
-0.0049
0.1908
0.2377
0.3542
-0.0782
0.1705
0.0864
0.0196
0.2616
-0.0606
0.2017
0.8989
185.6719
57.8771
43
2.8275
-5.1444
-3.8975
35.9764
14.8791
7.6538
-0.1238
-0.0284
-0.0546
-1.2328
-0.2307
1.0086
-0.2609
-0.0331
0.3545
0.2944
0.0394
0.0155
0.0977
0.0359
0.1389
-16.0313
163.9146
59.7551
44
5.3582
5.0924
0.7863
5.0247
0.7216
0.1189
-0.3653
0.6275
0.7795
-0.054
0.3363
1.0482
-0.0816
0.1225
0.0289
0.7717
-0.243
0.3014
0.3502
-0.2865
0.6371
-12.639
138.1017
47.1896
45
1.2071
-1.7344
-1.3115
15.7023
10.4813
7.1637
-0.0698
-0.233
-0.1695
-1.3765
0.6076
-0.6692
-0.7734
0.4558
-0.5377
0.4773
-0.0154
0.23
0.0562
-0.0249
0.4119
-3.8854
136.2466
50.6515
46
2.4002
-4.1432
-3.9967
24.9337
9.4213
7.0213
-0.1737
-0.752
0.2446
-0.1035
0.7917
-1.6548
0.1947
1.1569
-0.618
0.1361
0.1421
0.0386
0.3237
0.0299
0.2582
-8.9633
161.9906
66.1422
47
3.8418
-0.0884
-2.2548
1.105
0.3467
1.4068
-0.0909
-0.2507
-0.0259
0.1879
0.095
-0.1266
0.0754
0.1552
-0.0041
0.2551
0.1148
-0.058
0.2293
-0.0266
0.1149
0.8228
186.3165
61.1861
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
2 - 23
2
X-RAY DIFFRACTION
2
A
24 - 43
3
X-RAY DIFFRACTION
3
A
44 - 62
4
X-RAY DIFFRACTION
4
A
63 - 83
5
X-RAY DIFFRACTION
5
A
84 - 103
6
X-RAY DIFFRACTION
6
A
104 - 144
7
X-RAY DIFFRACTION
7
B
2 - 23
8
X-RAY DIFFRACTION
8
B
24 - 43
9
X-RAY DIFFRACTION
9
B
44 - 62
10
X-RAY DIFFRACTION
10
B
63 - 83
11
X-RAY DIFFRACTION
11
B
84 - 103
12
X-RAY DIFFRACTION
12
B
104 - 144
13
X-RAY DIFFRACTION
12
C
2 - 23
14
X-RAY DIFFRACTION
13
C
24 - 43
15
X-RAY DIFFRACTION
14
C
44 - 62
16
X-RAY DIFFRACTION
15
C
63 - 83
17
X-RAY DIFFRACTION
16
C
84 - 103
18
X-RAY DIFFRACTION
17
C
104 - 144
19
X-RAY DIFFRACTION
18
D
2 - 23
20
X-RAY DIFFRACTION
19
D
24 - 43
21
X-RAY DIFFRACTION
20
D
44 - 62
22
X-RAY DIFFRACTION
21
D
63 - 83
23
X-RAY DIFFRACTION
22
D
84 - 103
24
X-RAY DIFFRACTION
23
D
104 - 144
25
X-RAY DIFFRACTION
24
E
2 - 23
26
X-RAY DIFFRACTION
25
E
24 - 43
27
X-RAY DIFFRACTION
26
E
44 - 62
28
X-RAY DIFFRACTION
27
E
63 - 83
29
X-RAY DIFFRACTION
28
E
84 - 103
30
X-RAY DIFFRACTION
29
E
104 - 144
31
X-RAY DIFFRACTION
30
F
2 - 23
32
X-RAY DIFFRACTION
31
F
24 - 43
33
X-RAY DIFFRACTION
32
F
44 - 62
34
X-RAY DIFFRACTION
33
F
63 - 83
35
X-RAY DIFFRACTION
34
F
84 - 103
36
X-RAY DIFFRACTION
35
F
104 - 144
37
X-RAY DIFFRACTION
36
G
2 - 23
38
X-RAY DIFFRACTION
37
G
24 - 43
39
X-RAY DIFFRACTION
38
G
44 - 62
40
X-RAY DIFFRACTION
39
G
63 - 83
41
X-RAY DIFFRACTION
40
G
84 - 103
42
X-RAY DIFFRACTION
41
G
104 - 144
43
X-RAY DIFFRACTION
42
H
2 - 23
44
X-RAY DIFFRACTION
43
H
24 - 43
45
X-RAY DIFFRACTION
44
H
44 - 62
46
X-RAY DIFFRACTION
45
H
63 - 83
47
X-RAY DIFFRACTION
46
H
84 - 103
48
X-RAY DIFFRACTION
47
H
104 - 144
+
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