Resolution: 1.65→1.74 Å / Redundancy: 6 % / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 2.8 / Num. unique all: 5190 / % possible all: 100
-
Processing
Software
Name
Classification
Blu-Ice
datacollection
REFMAC
refinement
XDS
datareduction
XSCALE
datascaling
REFMAC
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: P6222 incomplete SeMAD model at 2.8 A resolution. Resolution: 1.65→18.8 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.507 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.19505
1729
4.8 %
RANDOM
Rwork
0.15741
-
-
-
obs
0.15926
34228
99.35 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 23.526 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.45 Å2
0 Å2
0 Å2
2-
-
0.15 Å2
0 Å2
3-
-
-
0.3 Å2
Refine analyze
Free
Obs
Luzzati coordinate error
0.094 Å
0.092 Å
Refinement step
Cycle: LAST / Resolution: 1.65→18.8 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2474
0
22
253
2749
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.014
0.022
2630
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1801
X-RAY DIFFRACTION
r_angle_refined_deg
1.494
1.976
3575
X-RAY DIFFRACTION
r_angle_other_deg
0.849
3
4421
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.754
5
335
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
40.588
25.203
123
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.408
15
439
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19.354
15
7
X-RAY DIFFRACTION
r_chiral_restr
0.093
0.2
359
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.021
2954
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
513
X-RAY DIFFRACTION
r_mcbond_it
1.911
3
1598
X-RAY DIFFRACTION
r_mcbond_other
0.568
3
657
X-RAY DIFFRACTION
r_mcangle_it
3.055
5
2572
X-RAY DIFFRACTION
r_scbond_it
4.69
8
1032
X-RAY DIFFRACTION
r_scangle_it
6.805
11
993
LS refinement shell
Resolution: 1.65→1.69 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.284
117
-
Rwork
0.251
2385
-
obs
-
-
96.19 %
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
2.3955
-1.1104
-0.3732
6.349
9.739
14.3706
0.0688
0.5498
0.2922
-0.5266
0.1845
-0.2963
-0.9252
0.222
-0.2533
0.1649
-0.032
0.0161
0.181
0.0819
0.1537
26.428
28.229
2.543
2
2.8501
-0.8564
-0.1761
7.7728
11.0066
14.1902
-0.0341
0.4642
0.1938
-0.5273
0.1121
-0.0886
-0.8829
0.1823
-0.078
0.2111
-0.0089
-0.0013
0.1421
0.0701
0.1162
24.798
25.381
4.973
3
1.8951
-1.7329
1.9392
5.7496
-1.6127
4.3039
0.31
0.3882
-0.2635
-0.3203
-0.3587
-0.0573
0.2222
-0.0015
0.0487
0.194
0.0463
-0.0533
0.2629
-0.0664
0.1319
20.836
8.074
0.194
4
7.8193
-2.7505
8.949
5.0746
-10.1346
19.1688
0.3823
-0.3402
-0.0967
-0.145
0.2257
1.2222
0.0553
-1.2184
-0.608
0.2195
-0.104
0.056
0.1775
-0.0895
0.5764
12.263
5.509
3.903
5
3.3519
0.2573
3.592
3.7526
1.7877
5.703
0.3296
0.2828
-0.1422
-0.2953
-0.1359
0.0287
0.2805
0.0192
-0.1937
0.2024
0.0274
-0.0346
0.2311
0.0119
0.08
18.339
12.637
-3.216
6
2.2483
0.5992
0.5468
1.9098
1.2076
4.103
-0.0114
0.037
0.2029
-0.1428
-0.0255
-0.0816
-0.3091
0.0656
0.0369
0.1163
-0.001
-0.0154
0.0308
0.0365
0.1296
26.932
27.829
17.506
7
0.7936
0.6264
-0.4223
0.7687
-0.2758
0.8593
-0.0838
-0.0146
0.061
-0.1151
-0.0153
0.005
-0.0688
-0.1581
0.0991
0.0988
0.0102
-0.0114
0.0798
0.0107
0.0871
20.837
21.19
15.94
8
-0.2334
1.8813
-2.1866
4.3231
-4.2969
23.2417
-0.2566
0.2473
0.0956
0.0465
-0.0597
-0.0728
-0.5538
0.6536
0.3163
0.1778
-0.0472
-0.085
0.2182
0.0675
0.1513
12.948
23.873
0.402
9
1.8012
-0.7634
2.5602
0.4856
0.3659
9.7173
-0.162
0.2109
0.1676
-0.1388
-0.0326
0.0515
-0.1763
0.0625
0.1946
0.2155
-0.0157
-0.0654
0.1994
0.05
0.1833
11.2
24.64
-7.172
10
2.3707
-1.451
2.1891
3.0864
-0.7149
2.2957
0.2332
0.2075
-0.0776
-0.1968
-0.1302
-0.1227
-0.0279
-0.0395
-0.103
0.1552
0.0362
-0.0052
0.1039
-0.0058
0.0937
22.708
12.834
9.463
11
1.1809
0.1365
1.9355
0.8391
0.8721
3.362
0.1288
0.2346
-0.0116
-0.2524
-0.0867
0.0498
0.0905
0.0069
-0.0421
0.1981
0.0534
-0.0231
0.2149
0.0239
0.1141
17.548
15.774
-1.268
12
19.2838
3.8315
-4.0633
-10.4724
7.8893
8.7269
-0.4575
0.338
-0.8282
0.5829
0.7926
0.3765
0.4837
-0.6148
-0.335
0.3484
0.1114
-0.0731
0.5346
0.1331
0.1908
9.786
14.125
-13.224
13
0.5402
-0.3433
1.8305
0.6549
-0.011
8.8146
-0.062
0.2059
0.1369
-0.1316
-0.0113
0.0042
-0.2467
0.135
0.0733
0.1427
-0.0211
-0.0517
0.1837
0.0431
0.1581
15.659
26.012
-1.412
14
9.7785
3.9952
8.667
2.4944
-2.9599
28.7701
0.0735
-0.26
0.5596
0.1637
0.1072
0.1538
-0.154
-1.2511
-0.1807
0.0886
0.035
-0.0086
0.1634
0.0127
0.1725
11.007
23.648
19.184
15
9.9282
2.4353
5.4798
1.4749
0.3595
9.1366
-0.112
-0.0995
0.3304
0.1789
-0.0438
0.2081
-0.4921
-0.1199
0.1558
0.1487
0.0294
0.017
0.1077
-0.0185
0.1758
16.076
28.867
29.422
16
6.471
-1.2368
7.0005
3.9373
-6.6634
24.7558
-0.2075
-0.5016
0.5132
0.3012
-0.2725
-0.0574
-1.0492
-0.1109
0.48
0.1718
0.0121
-0.0369
0.145
-0.08
0.1902
20.883
32.033
33.007
17
-2.0375
1.7193
7.1029
12.0438
2.4414
29.7027
0.0462
0.0792
0.1833
0.1558
-0.0106
-0.1247
-0.3506
-0.8867
-0.0356
0.1788
0.0731
-0.0253
0.1517
-0.003
0.2318
14.979
32.87
18.547
18
3.4312
-0.3691
-11.397
3.9565
5.0761
45.8747
-0.1742
0.4072
0.0297
-0.121
-0.1386
0.2486
-0.8347
-1.2591
0.3128
0.2763
0.0287
-0.0735
0.1333
0.0034
0.1826
14.306
32.638
7.324
19
-1.0312
1.5002
-0.1571
7.3629
9.7074
27.1498
-0.2454
0.4065
0.3113
-0.2744
0.09
0.2267
-0.6908
0.9274
0.1554
0.1134
-0.1187
-0.0805
0.4421
0.1077
0.208
21.003
29.662
-4.481
20
7.9314
-7.5143
-4.5437
16.0845
5.3848
11.7721
-0.5148
0.0219
0.241
-0.4359
0.0098
-0.656
0.536
1.6371
0.5049
0.1668
0.0645
0.0055
0.4325
0.097
0.1514
23.955
19.38
-11.314
21
0.2633
0.0433
0.3119
0.1051
-0.0203
0.4963
-0.003
0.0496
0.0189
-0.0283
-0.0043
0.0159
-0.0308
-0.022
0.0073
0.1482
0.0013
-0.0025
0.1415
0.0069
0.135
18.1543
24.0922
4.6456
22
14.5294
-3.7862
6.5876
12.9764
2.345
3.3018
-0.3884
-0.8144
0.3073
0.2436
0.5303
-1.2517
0.0529
-0.0976
-0.1419
0.029
0.0197
-0.0172
0.2142
0.0031
0.0681
27.941
12.902
38.833
23
2.6658
6.5305
6.3235
14.4255
14.7013
17.339
0.5656
-0.1959
-0.3803
0.3443
-0.2872
-0.517
0.3355
-0.4993
-0.2784
0.0987
-0.0376
-0.0352
0.106
0.0535
0.0672
28.085
3.567
28.275
24
0.4408
-0.165
-1.6086
4.5546
4.2804
7.1807
0.0722
-0.2259
0.0308
-0.0505
-0.1281
-0.3989
-0.0395
-0.2912
0.0558
0.026
-0.0005
0.014
0.1675
-0.0179
0.0887
25.876
11.329
31.886
25
5.8771
-4.703
6.0474
3.1665
-5.359
13.3376
-0.1112
-0.1225
0.3139
0.1887
0.0455
-0.2974
-0.5456
-0.0334
0.0657
0.102
-0.0067
-0.0124
0.1167
-0.0345
0.1512
17.364
25.237
38.554
26
25.5256
6.1184
-1.5364
2.9332
-8.8641
14.7927
0.3202
-0.1326
1.2171
0.2252
0.2786
0.6842
-0.1429
-0.588
-0.5988
0.0545
0.0692
0.049
0.1413
0.0272
0.2143
8.626
26.644
29.703
27
4.8442
-0.2233
0.8661
2.7217
-3.1026
3.6306
0.2162
-0.1124
0.0503
0.1946
-0.0046
0.2815
-0.0279
-0.0535
-0.2116
0.1201
0.0199
0.0128
0.1805
-0.0471
0.1001
10.85
22.544
40.452
28
6.186
0.0813
-3.9357
4.5408
3.6248
4.5144
0.0208
-0.3684
0.1614
0.2649
-0.079
-0.0991
0.1371
0.0906
0.0582
0.0618
0.0424
-0.0137
0.1271
0.0017
0.0548
20.435
17.119
34.203
29
4.53
-0.5911
-0.5607
1.0828
1.7595
1.5715
-0.1559
-0.1427
-0.3583
-0.0187
0.0041
0.0558
-0.0194
0.2069
0.1518
0.0466
0.0131
0.0431
0.0585
0.067
0.087
30.262
9.814
19.179
30
0.1656
-0.7137
0.0953
1.2226
-0.8699
1.9532
-0.0752
-0.0428
0.1398
-0.188
-0.0171
0.0048
-0.0216
-0.0549
0.0923
0.0824
0.0286
-0.0116
0.0215
0.0114
0.0818
21.187
14.035
20.438
31
1.7149
-0.222
3.1579
0.9671
-1.6151
11.18
0.0704
-0.3197
-0.1642
0.1929
0.016
0.1631
0.3483
-0.0683
-0.0864
0.1174
0.0253
0.0599
0.1716
0.0316
0.0807
14.582
6.691
41.828
32
7.9891
0.1942
5.5082
5.9286
-9.312
11.6306
0.2265
-0.333
-0.3806
-0.2722
0.0895
0.2079
1.0937
-0.7824
-0.316
0.2108
-0.066
0.1206
0.2437
-0.0374
0.1019
9.897
6.802
41.244
33
-0.1401
0.4821
-0.6426
2.2229
-1.2798
2.3042
0.0012
-0.1434
0.1309
0.0621
-0.0912
-0.0821
-0.0157
-0.081
0.0899
0.037
0.018
-0.011
0.0841
-0.0526
0.1184
18.639
19.87
27.979
34
0.8524
0.019
-1.0822
2.1501
-1.3412
1.8557
-0.0343
-0.154
-0.1088
0.2784
0.044
0.2503
-0.081
-0.0476
-0.0097
0.1188
-0.0045
0.0381
0.2158
-0.0152
0.1057
10.517
15.749
45.733
35
0.6736
0.1899
0.0287
0.9018
-0.1336
9.3819
-0.0082
-0.236
-0.0518
0.1053
0.0013
0.03
0.1126
0.0044
0.0069
0.0356
0.0087
0.0181
0.1072
0.0239
0.0635
17.912
6.346
34.747
36
4.4835
3.5086
-1.3073
8.4816
-0.9123
27.7973
0.0738
0.1121
-0.1291
0.0257
0.0931
-0.0589
0.7669
-1.5416
-0.1669
0.0633
-0.0225
-0.0249
0.1198
0.0216
0.0053
13.683
8.618
16.1
37
5.7279
-1.0627
-1.9167
3.8563
1.4488
2.027
0.1205
0.2013
-0.0828
-0.6132
-0.0964
-0.0864
-0.0256
-0.0306
-0.0241
0.1777
0.0296
0.0126
0.0555
-0.005
0.0629
23.95
4.929
4.701
38
0.4849
-0.8662
-3.4832
-0.3758
2.0789
10.8752
0.3886
0.25
0.3488
-0.139
0.4223
0.2097
0.1222
-0.5286
-0.8109
0.1351
0.0318
-0.0405
0.1421
0.1162
0.173
22.754
2.944
13.36
39
9.0317
-0.079
5.5281
1.2177
2.9
11.1377
0.0991
-0.1589
-0.5319
0.0604
0.045
0.0523
0.0971
-0.2659
-0.1442
0.0821
0.0063
0.0096
0.0555
0.0204
0.0891
18.572
0.282
27.277
40
2.4103
-0.1386
-6.4153
6.9366
7.9679
13.7427
-0.0847
-0.2097
0.004
0.3792
-0.0546
-0.1096
0.5469
-0.0305
0.1393
0.08
0.012
-0.0022
0.253
0.0077
0.0661
23.26
5.869
40.651
41
-0.5638
1.1399
1.6699
21.4158
5.4652
7.0568
-0.263
-0.5033
0.6544
0.5513
-0.2586
-0.8078
-0.3019
0.3144
0.5216
0.1058
-0.0162
-0.0182
0.2478
-0.001
0.179
21.625
16.416
48.253
42
0.3684
-0.1048
-0.2639
0.3237
0.036
0.5089
-0.0068
-0.0561
0
0.0265
-0.0006
0.006
0.0243
0.0004
0.0074
0.0972
-0.0017
-0.0072
0.1221
0.0069
0.1046
19.978
10.1939
31.5319
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
3 - 13
2
X-RAY DIFFRACTION
2
A
14 - 21
3
X-RAY DIFFRACTION
3
A
22 - 28
4
X-RAY DIFFRACTION
4
A
29 - 34
5
X-RAY DIFFRACTION
5
A
35 - 45
6
X-RAY DIFFRACTION
6
A
46 - 59
7
X-RAY DIFFRACTION
7
A
60 - 67
8
X-RAY DIFFRACTION
8
A
68 - 72
9
X-RAY DIFFRACTION
9
A
73 - 85
10
X-RAY DIFFRACTION
10
A
86 - 94
11
X-RAY DIFFRACTION
11
A
95 - 103
12
X-RAY DIFFRACTION
12
A
104 - 109
13
X-RAY DIFFRACTION
13
A
110 - 124
14
X-RAY DIFFRACTION
14
A
125 - 129
15
X-RAY DIFFRACTION
15
A
130 - 134
16
X-RAY DIFFRACTION
16
A
135 - 140
17
X-RAY DIFFRACTION
17
A
141 - 144
18
X-RAY DIFFRACTION
18
A
145 - 148
19
X-RAY DIFFRACTION
19
A
149 - 152
20
X-RAY DIFFRACTION
20
A
153 - 158
21
X-RAY DIFFRACTION
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1001 - 1116
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3 - 9
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10 - 13
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14 - 21
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22 - 26
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27 - 32
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33 - 41
28
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42 - 46
29
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47 - 60
30
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30
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61 - 67
31
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68 - 77
32
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32
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78 - 83
33
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33
B
84 - 96
34
X-RAY DIFFRACTION
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B
97 - 112
35
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35
B
113 - 124
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36
B
125 - 129
37
X-RAY DIFFRACTION
37
B
130 - 136
38
X-RAY DIFFRACTION
38
B
137 - 143
39
X-RAY DIFFRACTION
39
B
144 - 148
40
X-RAY DIFFRACTION
40
B
149 - 152
41
X-RAY DIFFRACTION
41
B
153 - 158
42
X-RAY DIFFRACTION
42
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1001 - 1137
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