suppression by virus of host cytokine production / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / negative regulation of miRNA-mediated gene silencing / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / suppression by virus of host type I interferon production / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / positive regulation of protein sumoylation ...suppression by virus of host cytokine production / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / negative regulation of miRNA-mediated gene silencing / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / suppression by virus of host type I interferon production / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / positive regulation of protein sumoylation / molecular sequestering activity / viral transcription / viral genome replication / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / viral nucleocapsid / host cell cytoplasm / negative regulation of gene expression / RNA binding Similarity search - Function
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9791209 Å / Relative weight: 1
Reflection
Resolution: 1.85→50 Å / Num. obs: 21610 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 7.8
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Diffraction-ID
% possible all
1.85-1.88
5.6
0.481
1
99.5
1.88-1.92
6.1
0.404
1
99.7
1.92-1.95
6.8
0.368
1
100
1.95-1.99
7
0.27
1
99.8
1.99-2.04
7.1
0.263
1
99.8
2.04-2.08
7.1
0.3
1
99.9
2.08-2.14
7.1
0.214
1
100
2.14-2.19
7.2
0.186
1
99.9
2.19-2.26
7.2
0.212
1
99.9
2.26-2.33
7.2
0.187
1
100
2.33-2.41
7.2
0.153
1
100
2.41-2.51
7.2
0.158
1
100
2.51-2.63
7.2
0.128
1
100
2.63-2.76
7.2
0.126
1
100
2.76-2.94
7.1
0.109
1
100
2.94-3.16
7.1
0.103
1
100
3.16-3.48
7.1
0.107
1
100
3.48-3.99
7
0.089
1
100
3.99-5.02
6.7
0.075
1
100
5.02-50
6.4
0.093
1
99.8
-
Phasing
Phasing
Method: molecular replacement
-
Processing
Software
Name
Version
Classification
NB
PHENIX
1.8.1_1168
refinement
SCALEPACK
datascaling
MOLREP
phasing
REFMAC
refinement
PDB_EXTRACT
3.11
dataextraction
HKL-3000
datacollection
DENZO
datareduction
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→41.898 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.18 / SU R Cruickshank DPI: 0.1737 / σ(F): 1.34 / Phase error: 29.49 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Rfree
0.2414
1088
5.1 %
Rwork
0.1925
-
-
obs
0.1949
21347
98.74 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Biso mean: 20.0469 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.01 Å2
0 Å2
0 Å2
2-
-
0 Å2
0 Å2
3-
-
-
0 Å2
Refinement step
Cycle: LAST / Resolution: 1.85→41.898 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1917
0
82
216
2215
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.007
2072
X-RAY DIFFRACTION
f_angle_d
1.183
2824
X-RAY DIFFRACTION
f_dihedral_angle_d
16.048
820
X-RAY DIFFRACTION
f_chiral_restr
0.061
304
X-RAY DIFFRACTION
f_plane_restr
0.005
368
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.8497-1.9338
0.2948
147
0.2411
2441
X-RAY DIFFRACTION
97
1.9338-2.0358
0.2709
114
0.2105
2489
X-RAY DIFFRACTION
98
2.0358-2.1633
0.2268
136
0.1872
2476
X-RAY DIFFRACTION
99
2.1633-2.3304
0.2361
146
0.1854
2498
X-RAY DIFFRACTION
98
2.3304-2.5648
0.2576
155
0.1893
2487
X-RAY DIFFRACTION
99
2.5648-2.9359
0.2381
127
0.1989
2547
X-RAY DIFFRACTION
99
2.9359-3.6986
0.247
138
0.1834
2600
X-RAY DIFFRACTION
100
3.6986-41.9084
0.2165
125
0.1866
2721
X-RAY DIFFRACTION
100
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
4.8727
1.5488
-1.0283
1.4287
0.2441
1.69
-0.0537
0.5072
-0.5019
-0.1755
0.0544
0.0951
0.3115
-0.3302
0.0952
0.1181
-0.0167
-0.014
0.123
-0.0343
0.1753
2.3073
22.3908
-11.9209
2
3.5519
-0.7375
-1.1052
0.1813
0.1089
2.1558
-0.2586
-0.0602
-0.4672
0.0413
0.1812
0.0559
0.1093
-0.0595
0.0701
0.0983
0.0105
0.0098
0.0605
-0.0069
0.0838
6.1406
25.8493
-4.1299
3
1.8106
0.1733
-1.1129
0.1575
-0.1259
2.3883
0.0552
0.1397
0.2108
0.0222
0.0401
0.0637
-0.1881
-0.0338
-0.1028
0.1051
0.0205
-0.008
0.0868
0.0122
0.1193
2.5776
35.3968
-9.6951
4
3.8098
-1.4147
-0.1074
0.9616
0.2013
2.0151
-0.2726
-0.6079
-0.5381
0.1344
0.1643
0.1184
0.5532
-0.0704
0.0333
0.1946
0.0244
0.0235
0.1229
0.041
0.1436
9.1708
20.8048
9.0351
5
2.5397
-0.1426
-0.5638
0.9219
-0.1129
3.6292
0.0083
-0.2771
0.0967
0.0273
0.0045
0.1735
-0.0731
-0.0296
-0.0068
0.101
-0.0026
0.0048
0.0973
-0.0144
0.1009
11.0019
30.4714
7.8119
6
3.0423
-0.3176
-0.6731
0.9419
0.4375
2.4739
-0.0367
-0.2177
-0.588
0.0098
0.065
-0.2549
0.394
0.3588
0.1309
0.1507
0.0129
-0.0244
0.0933
0.0549
0.2435
-1.6209
22.0014
35.3214
7
4.0407
0.4407
-1.2052
0.0978
0.0787
2.5184
-0.0245
0.0772
-0.3593
-0.1259
0.0718
-0.0422
0.0721
-0.0346
0.0956
0.1069
-0.0091
0.0026
0.0429
-0.0046
0.0758
-6.25
25.6629
27.289
8
4.6011
-0.6215
-2.7919
0.5915
0.1759
3.8608
-0.0903
-0.437
0.1249
0.109
0.1388
-0.0611
0.1776
0.1539
-0.0586
0.0795
-0.004
-0.0067
0.123
-0.0059
0.0793
0.0637
32.7916
37.1894
9
3.2553
0.2167
-3.5125
0.097
-0.3648
3.9819
0.2701
-0.163
0.5802
0.0244
0.0821
-0.0434
-0.3445
0.0353
-0.1278
0.1141
-0.0059
0.0091
0.0953
-0.0091
0.1343
-8.0747
36.5633
33.4558
10
1.9544
0.5118
0.7107
0.8849
0.2781
4.5353
-0.1349
-0.2441
0.4459
-0.16
-0.0945
0.2516
-0.4601
0.5143
-0.0569
0.1373
-0.0473
0.0011
0.1553
-0.0275
0.155
1.11
37.7163
23.5875
11
5.4301
4.558
1.7483
6.1476
0.2826
1.9608
0.0256
0.0921
-0.5074
-0.2007
-0.0913
0.0625
0.2648
-0.0145
0.0228
0.1224
0.0246
0.001
0.0873
-0.0307
0.1232
-3.7902
23.8746
13.7889
12
1.6913
-1.3001
-0.6748
2.449
1.4294
3.6945
-0.1512
0.3273
-0.2618
0.1778
0.1888
0.0432
0.5306
-0.2231
0.1472
0.1709
-0.0406
0.0222
0.1375
-0.0271
0.1786
-15.6897
21.302
16.9587
13
0.7129
0.1497
-0.1252
0.5422
0.2777
2.3166
-0.0849
0.0201
0.3224
0.1593
-0.0632
-0.2095
-0.4763
-0.0005
-0.1385
0.1465
-0.0279
-0.0424
0.0939
0.047
0.1503
-9.7847
36.4758
12.9156
14
2.827
0.3806
-0.2193
0.6839
0.1499
4.1973
0.0363
0.2082
0.126
0.07
0.0178
-0.0339
0.0325
0.0576
-0.0225
0.0792
0.0134
0.0098
0.0853
0.0111
0.0818
-8.9971
30.0738
14.7908
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
chain 'A' and (resid218through231 )
2
X-RAY DIFFRACTION
2
chain 'A' and (resid232through252 )
3
X-RAY DIFFRACTION
3
chain 'A' and (resid253through292 )
4
X-RAY DIFFRACTION
4
chain 'A' and (resid293through304 )
5
X-RAY DIFFRACTION
5
chain 'A' and (resid305through340 )
6
X-RAY DIFFRACTION
6
chain 'B' and (resid217through231 )
7
X-RAY DIFFRACTION
7
chain 'B' and (resid232through252 )
8
X-RAY DIFFRACTION
8
chain 'B' and (resid253through269 )
9
X-RAY DIFFRACTION
9
chain 'B' and (resid270through283 )
10
X-RAY DIFFRACTION
10
chain 'B' and (resid284through292 )
11
X-RAY DIFFRACTION
11
chain 'B' and (resid293through297 )
12
X-RAY DIFFRACTION
12
chain 'B' and (resid298through310 )
13
X-RAY DIFFRACTION
13
chain 'B' and (resid311through319 )
14
X-RAY DIFFRACTION
14
chain 'B' and (resid320through340 )
+
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