Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97923 Å / Relative weight: 1
Reflection
Resolution: 1.85→30 Å / Num. all: 47314 / Num. obs: 47253 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 13.8
Reflection shell
Resolution: 1.85→1.88 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.724 / Mean I/σ(I) obs: 1.98 / Num. unique all: 2354 / % possible all: 100
-
Processing
Software
Name
Version
Classification
SBC-Collect
datacollection
PHENIX
modelbuilding
SHELXD
phasing
PHASER
phasing
PHENIX
(phenix.refine: 1.8_1069)
refinement
HKL-3000
datareduction
HKL-3000
datascaling
PHENIX
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.85→30.012 Å / SU ML: 0.17 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 18.83 / Stereochemistry target values: ML / Details: HYDROGEN ATOMS HAVE BEEN ADDED AT RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1982
1212
2.57 %
random
Rwork
0.1496
-
-
-
all
0.1509
47227
-
-
obs
0.1509
47227
99.78 %
-
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement step
Cycle: LAST / Resolution: 1.85→30.012 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4826
0
0
280
5106
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.014
4932
X-RAY DIFFRACTION
f_angle_d
1.395
6735
X-RAY DIFFRACTION
f_dihedral_angle_d
13.103
1753
X-RAY DIFFRACTION
f_chiral_restr
0.087
807
X-RAY DIFFRACTION
f_plane_restr
0.007
864
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.85-1.9241
0.218
133
0.1918
5091
X-RAY DIFFRACTION
99
1.9241-2.0116
0.2417
133
0.1839
5027
X-RAY DIFFRACTION
100
2.0116-2.1177
0.2375
124
0.1698
5133
X-RAY DIFFRACTION
100
2.1177-2.2503
0.2503
135
0.1623
5079
X-RAY DIFFRACTION
100
2.2503-2.424
0.1987
144
0.1546
5102
X-RAY DIFFRACTION
100
2.424-2.6678
0.2178
133
0.1532
5113
X-RAY DIFFRACTION
100
2.6678-3.0535
0.2251
140
0.1554
5125
X-RAY DIFFRACTION
100
3.0535-3.8458
0.1732
143
0.1394
5143
X-RAY DIFFRACTION
100
3.8458-30.0157
0.1625
127
0.1322
5202
X-RAY DIFFRACTION
99
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
0.7135
0.8001
-0.3466
0.8631
-0.4012
0.1684
-0.2038
0.2685
-0.1359
-0.3946
0.2545
-0.1088
0.0674
-0.0035
0.0005
0.2297
-0.0296
-0.0026
0.2093
-0.0019
0.2424
46.9117
15.5895
54.8917
2
0.7523
-0.0061
0.6185
2.2966
-0.2154
0.919
0.0158
-0.0899
0.1129
0.1604
0.0158
-0.0361
0.0077
-0.0229
0
0.1297
-0.0066
-0.0109
0.1428
0.0003
0.1882
46.7331
12.97
73.7702
3
0.4751
-0.0592
0.15
0.6742
-0.438
1.0895
-0.0377
-0.053
0.0184
-0.0987
0.0077
0.142
-0.1008
-0.1498
0
0.1536
-0.0068
0.0059
0.1311
-0.0015
0.1696
42.5981
21.8598
65.029
4
0.5323
0.2208
-0.0801
0.2083
0.0713
0.1724
0.0437
0.1887
0.086
-0.2279
0.0463
0.1013
-0.1567
-0.1276
0.0052
0.1997
-0.0078
0.004
0.1631
0.0033
0.1304
33.2982
6.2195
53.2559
5
0.9709
-0.2468
-0.3415
1.0869
-0.6224
0.6091
0.0163
0.1609
0.1421
0.0671
-0.0613
-0.0457
-0.1066
-0.0157
0.0001
0.1713
0.0175
-0.0179
0.1832
0.0119
0.1856
16.5349
9.7353
68.3546
6
0.2281
-0.0803
-0.0006
0.8273
0.2816
0.4673
0.0186
-0.0396
0.154
0.0257
-0.0639
-0.0148
-0.1667
-0.1799
0
0.1856
0.0342
-0.0139
0.2062
0.0083
0.2092
13.6185
11.9169
69.5265
7
0.2268
-0.1058
-0.061
1.1722
0.1183
1.5368
0.1057
-0.3683
-0.192
0.2681
-0.1536
0.1204
0.053
-0.0636
-0.0001
0.1704
-0.0079
0.0137
0.1748
0.0137
0.1722
17.1195
0.5462
75.7297
8
1.3807
0.2251
-0.252
0.3119
-0.1939
0.9167
-0.0628
-0.0214
-0.2055
0.0478
0.0428
0.0064
0.0815
-0.074
0
0.119
-0.0058
-0.0017
0.0964
-0.0152
0.1365
29.8528
-1.07
62.2271
9
0.2201
0.2576
-0.0305
0.4151
-0.1772
0.1458
-0.1782
-0.5302
-0.234
0.2841
0.2594
-0.0786
0.0623
0.0348
-0.0016
0.3188
0.0617
0.0324
0.3177
0.0387
0.3294
1.9968
30.507
69.5636
10
0.7068
0.003
0.2124
2.3422
0.3981
1.082
0.0224
0.1785
0.081
-0.3049
0.0072
0.0426
-0.0139
-0.057
-0.0001
0.1606
0.0271
-0.0083
0.1719
-0.001
0.1594
-3.1804
42.2903
46.7154
11
1.1255
0.2289
-0.3368
1.0314
0.6525
1.4858
0.125
0.1405
0.2069
-0.1116
-0.0334
-0.0992
-0.3199
0.0502
0.0074
0.1691
0.0303
0.013
0.127
0.0175
0.1744
0.4876
49.0053
53.3143
12
0.3894
-0.1442
-0.1457
0.3193
-0.0795
0.3583
-0.0627
-0.406
-0.1268
0.0659
0.0202
-0.0165
-0.1542
0.0892
0.0017
0.168
0.0147
0.0059
0.1718
0.0084
0.1249
12.1549
33.8762
65.4853
13
1.0207
0.3153
-0.2647
0.9559
0.3604
0.3073
-0.0573
-0.1244
0.1354
-0.0579
-0.1125
-0.011
-0.1888
0.1989
0.0007
0.1596
0.0073
-0.0122
0.2162
-0.0069
0.1428
28.7855
38.5208
49.4377
14
0.146
-0.107
-0.1728
0.2953
0.06
0.2228
-0.1504
-0.1901
0.297
0.0932
0.048
0.0987
-0.1735
0.0831
-0.0004
0.228
0.035
-0.0124
0.2237
0.0171
0.2253
23.5755
39.8539
56.0765
15
1.5274
0.5733
-0.1961
1.4613
-0.3347
2.4113
0.02
0.1222
-0.0741
-0.2091
-0.0805
-0.1908
0.0559
0.3571
-0.0002
0.1567
0.03
0.0018
0.2324
-0.0141
0.137
30.8359
34.9502
44.8492
16
1.0685
-0.0316
-0.2716
0.3473
-0.2239
0.6718
0.0206
0.0832
-0.1336
-0.0054
-0.0674
-0.0243
0.1016
0.1447
0
0.1387
0.041
-0.0033
0.1276
-0.0008
0.1373
14.2296
27.3869
56.2011
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
(chainAandresid39:72)
2
X-RAY DIFFRACTION
2
(chainAandresid73:142)
3
X-RAY DIFFRACTION
3
(chainAandresid143:184)
4
X-RAY DIFFRACTION
4
(chainAandresid185:205)
5
X-RAY DIFFRACTION
5
(chainAandresid206:231)
6
X-RAY DIFFRACTION
6
(chainAandresid232:268)
7
X-RAY DIFFRACTION
7
(chainAandresid269:308)
8
X-RAY DIFFRACTION
8
(chainAandresid309:354)
9
X-RAY DIFFRACTION
9
(chainBandresid32:55)
10
X-RAY DIFFRACTION
10
(chainBandresid56:141)
11
X-RAY DIFFRACTION
11
(chainBandresid142:186)
12
X-RAY DIFFRACTION
12
(chainBandresid187:207)
13
X-RAY DIFFRACTION
13
(chainBandresid208:229)
14
X-RAY DIFFRACTION
14
(chainBandresid230:242)
15
X-RAY DIFFRACTION
15
(chainBandresid243:305)
16
X-RAY DIFFRACTION
16
(chainBandresid306:354)
+
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