Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.1 Å3/Da / Density % sol: 41.5 % / Description: NONE
Crystal grow
Method: vapor diffusion, sitting drop Details: SITTING DROP VAPOUR DIFFUSION SYSTEM, MICROLITER DROPS OF PURIFIED P23-77 VIRION (PROTEIN CONCENTRATION 2.4 MG/ML, SAMPLE BUFFER 20 MM TRIS-HCL PH 7.5, 5 MM MGCL2 AND 150 MM NACL) MIXED 1:1 ...Details: SITTING DROP VAPOUR DIFFUSION SYSTEM, MICROLITER DROPS OF PURIFIED P23-77 VIRION (PROTEIN CONCENTRATION 2.4 MG/ML, SAMPLE BUFFER 20 MM TRIS-HCL PH 7.5, 5 MM MGCL2 AND 150 MM NACL) MIXED 1:1 WITH SOLUTION CONSISTING OF 0.1 M CITRIC ACID PH 3.5, 20 MM TRIS-HCL PH 7.5, 5 MM MGCL2, 150 MM NACL AND 25%(W/V) PEG 3350.
Resolution: 2.36→42.16 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.9101 / SU R Cruickshank DPI: 0.449 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.472 / SU Rfree Blow DPI: 0.246 / SU Rfree Cruickshank DPI: 0.248 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY. RESIDUES 1 AND 171- 173 ARE DISORDERED IN CHAIN A, RESIDUES 1 AND 170-173 ARE DISORDERED IN CHAIN B, ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY. RESIDUES 1 AND 171- 173 ARE DISORDERED IN CHAIN A, RESIDUES 1 AND 170-173 ARE DISORDERED IN CHAIN B, RESIDUES 1 AND 169-173 ARE DISORDERED IN CHAINS C AND F, RESIDUES 1, 124- -129 AND 169-173 ARE DISORDERED IN CHAIN D, RESIDUES 1 AND 168-173 ARE DISORDERED IN CHAIN E, RESIDUES 1-3 AND 169- -173 ARE DISORDERED IN CHAIN G, RESIDUES 1, 123-127 AND 169-173 ARE DISORDERED IN CHAIN H.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2344
2743
5.08 %
RANDOM
Rwork
0.1925
-
-
-
obs
0.1946
53974
98.59 %
-
Displacement parameters
Biso mean: 52.25 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-10.2165 Å2
0 Å2
0 Å2
2-
-
-0.8751 Å2
0 Å2
3-
-
-
11.0916 Å2
Refine analyze
Luzzati coordinate error obs: 0.308 Å
Refinement step
Cycle: LAST / Resolution: 2.36→42.16 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
10375
0
4
348
10727
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.01
10632
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1.07
14517
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
3545
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
259
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
1538
HARMONIC
5
X-RAY DIFFRACTION
t_it
10632
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
X-RAY DIFFRACTION
t_omega_torsion
3.13
X-RAY DIFFRACTION
t_other_torsion
16.27
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
1356
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_sum_occupancies
X-RAY DIFFRACTION
t_utility_distance
X-RAY DIFFRACTION
t_utility_angle
X-RAY DIFFRACTION
t_utility_torsion
X-RAY DIFFRACTION
t_ideal_dist_contact
11421
SEMIHARMONIC
4
LS refinement shell
Resolution: 2.36→2.42 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.2862
224
5.72 %
Rwork
0.2286
3691
-
all
0.2318
3915
-
obs
-
-
98.59 %
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
0.2813
-0.3248
-0.0583
0.2575
0.4575
0.0346
-0.002
0.0124
-0.0037
0.0007
0.0018
0.0081
0.0037
0.0178
0.0002
0.0259
0.088
0.0279
-0.0213
-0.0901
-0.0019
27.0264
-10.5281
-121.672
2
0.9284
0.0774
-0.6556
0.4887
-0.2203
2.2162
0.0202
0.0247
-0.0231
-0.1497
-0.0081
0.0265
0.0205
-0.0778
-0.0121
-0.0829
0.0089
-0.0313
-0.1087
-0.0158
0.0419
5.273
0.7999
-98.729
3
0.6404
-0.2764
-1.0606
1.0112
-0.0517
1.0401
-0.0016
-0.0201
-0.046
-0.0054
0.044
0.0898
0.0339
-0.0117
-0.0423
-0.1108
-0.0261
-0.0343
-0.0191
0.0094
0.0515
-1.4554
-3.6334
-89.8306
4
0
-0.2318
-0.4318
0.0964
0.2167
0.0178
0.0016
0.0117
-0.0071
-0.0187
-0.0003
-0.0034
0.0265
-0.0033
-0.0014
0.0438
-0.0454
-0.034
-0.0288
-0.0204
0.0177
4.5866
-14.2742
-95.9037
5
0.8716
-0.0911
-0.3119
0.0001
0.0469
1.4462
0.0168
-0.0027
0.0144
0.0237
-0.0151
0.0158
-0.0817
0.019
-0.0017
-0.0429
0.0336
-0.0454
-0.0483
-0.0168
0.0202
5.4408
-0.9713
-86.2442
6
0.196
0.0758
0.0589
0.0741
-0.2788
0.014
0.0035
0.0065
0
0.0085
0.0147
0.0077
0.0067
0.0122
-0.0182
-0.0359
-0.0507
0.022
-0.002
0.0225
0.0328
1.6034
-17.5731
-79.0624
7
0.6512
0.0816
-0.5289
0.0065
-0.0575
3.1788
0.0193
0.01
-0.0086
-0.0526
0.0166
-0.0122
-0.0327
0.0493
-0.0359
-0.0213
0.026
-0.0161
-0.1162
0.0048
0.0168
14.3453
3.0205
-102.227
8
0.3891
-0.1794
-1.1736
0.0154
-0.7543
1.8972
0.0111
0.0375
-0.0177
-0.0436
0.0389
-0.0109
0.0219
0.1171
-0.05
-0.0116
0.008
-0.0081
-0.0112
-0.0167
-0.0158
23.3806
2.968
-110.884
9
0.091
-0.7017
-0.0423
0
-0.6437
0.0031
-0.0021
-0.0061
0.0115
0.0051
-0.0139
-0.0048
0.0073
-0.0028
0.0159
0.0136
0.0284
0.002
0.0061
0.0607
-0.0023
21.8081
-10.9867
-103.592
10
0.7619
0.5421
0.1296
0
-0.0804
2.8882
0.0051
0.0567
-0.0018
-0.0235
-0.0234
0.0041
0.0329
-0.0428
0.0183
-0.0045
0.0282
-0.0271
-0.0515
-0.0123
-0.0003
15.4103
2.0148
-114.203
11
0.0811
-0.0338
-0.0508
0
0.066
0.2244
-0.0009
-0.015
0.0013
-0.0038
-0.002
-0.0106
-0.0007
-0.0102
0.003
0.0238
0.0229
0.0154
0.0058
0.0228
-0.037
-1.9276
13.6174
19.2733
12
0.0027
0.2945
-0.2794
0.5684
0.3779
1.1654
0.0063
-0.0479
-0.0406
0.0898
-0.0043
0.0035
-0.0081
0.062
-0.002
0.0173
0.0433
-0.0129
-0.0076
0.0214
-0.047
18.9017
-5.0259
-2.0217
13
0.8581
-0.2352
0.2214
0.0089
-0.1378
2.1038
0.0125
0.0557
-0.0703
0.0177
0.0421
-0.0088
0.0162
-0.0155
-0.0546
0.0087
-0.002
0.0079
-0.0186
0.0079
-0.0248
17.4259
-11.3669
-7.214
14
0.5792
1.2183
-0.3304
0.3682
0.3237
0.0257
0.0052
-0.0239
-0.0142
0.0002
0.001
-0.003
0.0348
0.0024
-0.0061
0.0076
0.0151
0.0151
-0.0394
0.0001
0.0123
11.0037
-18.3398
-6.1798
15
0.4928
-0.5506
0.8294
1.8677
-0.2862
1.9091
-0.0009
0.0398
0.0067
0.0207
0.0492
0.0308
-0.0793
0.0152
-0.0483
0.0485
0.0283
0.016
-0.0452
0.0295
-0.0575
16.1238
-7.7488
-10.9992
16
0.1714
0.3784
0.2646
0.0291
0.194
0.3737
-0.0004
0.0194
-0.0125
-0.0097
-0.0039
0.0125
-0.0025
-0.0165
0.0042
-0.0065
0.0068
-0.0316
0.03
-0.017
-0.0203
2.3681
-16.7002
-19.3179
17
0.3873
0.1433
0.1312
0.9056
1.3289
2.1886
0.0224
0.0562
0.0371
0.0242
0.025
0.0455
-0.036
-0.0109
-0.0474
0.1003
0.0242
-0.0132
-0.0934
0.0446
-0.0542
16.5853
7.5172
4.0095
18
0.0199
0.1176
-0.0025
0.0551
0.0204
0
0.0002
-0.0021
0.0085
0.005
-0.0017
0.0044
-0.0056
-0.0072
0.0015
-0.004
0.0159
0.0129
-0.0157
-0.0039
0.0398
11.8222
27.5416
13.206
19
0.7522
0.4061
0.0126
0.0162
0.7513
1.9275
-0.0043
0.0052
-0.001
0.0197
0.0393
0.001
-0.0143
-0.044
-0.035
0.0321
0.0181
-0.0005
-0.0563
0.0303
-0.0247
14.9313
9.6092
9.3162
20
0.0016
-0.4706
-0.3712
0.453
0.2001
0.2573
0.001
-0.0087
-0.0022
-0.0054
-0.0081
0.007
-0.0003
-0.0175
0.0071
0.0313
-0.0207
0.0547
-0.0266
-0.0106
-0.0164
7.1632
9.4402
19.539
21
0.0365
0.0146
-0.3052
0.2824
0.0019
0
-0.0004
0.0114
0.0062
-0.0008
0.0003
-0.0009
-0.0052
0.0045
0.0001
0.0245
-0.0121
0.0376
-0.0568
0.029
0.0295
8.3083
17
-69.1617
22
0.7402
-0.0867
0.3721
0
-0.4148
3.8217
0.0085
-0.0366
0.0419
0.0187
0.0561
0.0273
0.1372
0.103
-0.0646
0.0698
-0.0289
-0.0085
-0.0684
-0.0322
-0.0692
14.8222
-8.1101
-48.267
23
0.0004
-0.7945
0.7435
0.0105
-0.4172
1.3691
0.0001
-0.0048
-0.0117
-0.001
0.0035
-0.0084
-0.0235
0.0144
-0.0036
0.0667
-0.0019
-0.009
0.0158
-0.0451
-0.0972
14.7941
-0.1768
-43.9888
24
0.4148
-0.2675
-0.7474
0.1084
-0.0053
1.0671
-0.0055
0.0365
-0.0057
-0.019
0.0206
-0.0181
0.0234
0.0434
-0.0151
0.0425
0.1193
-0.0179
0.0836
0.0023
-0.1157
28.8635
-13.9745
-39.7101
25
0.1894
-0.0803
0.1031
1.4726
-0.4115
4.7305
0.0079
-0.0044
0.0109
-0.026
0.0338
0.0102
0.069
0.0474
-0.0417
0.1089
0.0039
-0.0214
-0.0094
-0.0084
-0.1303
17.9658
-7.8087
-37.6506
26
0.1045
-0.0226
0.0265
0
0.1001
0.1941
-0.0012
0.0007
0.0064
0.0011
-0.0023
0.0025
-0.0002
0.009
0.0035
0.0051
0.0015
-0.012
0.036
0.0131
-0.0385
32.7838
-0.0822
-29.6508
27
0.4188
-0.3076
0.7166
0.1509
-0.404
2.3972
0.0091
-0.0692
-0.0263
0.0884
0.0304
0.0219
0.067
-0.0422
-0.0395
0.016
-0.0242
0.0027
-0.0463
-0.0006
-0.0395
5.6848
-0.838
-52.9037
28
0.004
0.1973
-0.0633
1.4836
0.5005
0.4395
0.005
-0.0043
0.023
0.021
-0.0034
0.0193
-0.0189
-0.0095
-0.0017
0.0228
-0.0035
-0.0253
-0.0263
-0.0249
0.0142
0.7413
12.0983
-58.2205
29
0.2929
-1.2242
0.6504
1.6577
-1.0245
1.6179
-0.0062
-0.0555
-0.0113
0.0078
0.0208
0.0172
0.0722
0.0054
-0.0147
-0.0225
-0.0848
0.0008
-0.0047
-0.0352
-0.0585
5.4791
-0.1906
-59.7846
30
0.0537
-0.1714
0.1519
0.179
-0.3764
0.1476
-0.0001
0.0027
-0.0031
0.0007
0.0074
-0.0002
-0.0054
0.0069
-0.0073
0.0054
-0.0062
0.0209
0.0055
0.031
-0.0078
12.9644
8.7248
-72.0822
31
0.173
0.0269
-0.0143
0.0583
-0.0194
0.2202
0.0011
0.0005
0.0025
0.0015
-0.0039
-0.0038
-0.0041
0.0083
0.0027
0.0301
-0.0003
-0.0041
0.0487
0.0238
0.0127
52.8092
33.3238
-31.2208
32
0
-0.1129
0.0702
0.4493
-0.0983
2.3907
0.0167
-0.0697
-0.0065
0.0796
-0.05
-0.0343
0.0295
-0.0634
0.0333
0.0236
-0.0653
-0.0066
-0.0547
0.0207
-0.0191
26.7634
38.109
-51.8537
33
0.0005
-0.3035
0.13
0.2389
-0.4669
2.1179
0.0027
-0.0016
0.0439
0.0216
-0.014
0.0471
0.0383
0.0666
0.0113
0.0784
0.0091
0.0076
-0.0177
-0.0182
-0.0715
30.9447
40.1256
-55.5679
34
0.1991
-0.4077
0.2711
0.3465
-0.0785
0.1215
-0.0011
-0.0048
0.0103
-0.0013
0.0004
-0.0031
-0.0018
-0.0065
0.0006
0.0408
0.0134
-0.0137
-0.0313
0.0229
-0.0071
16.1293
54.6795
-64.4414
35
0
0.2736
0.5937
0.6393
0.4156
0.2492
0.006
-0.0171
0.0122
0.0169
-0.0069
-0.011
-0.021
-0.0044
0.0008
0.0614
-0.0391
-0.0142
-0.0136
-0.0168
-0.0452
32.5318
52.037
-56.6927
36
0.0776
0.0059
-0.2291
0.4483
-0.2752
3.1662
0.0014
0.0329
0.004
0.0488
-0.0141
0.0105
0.0524
-0.0008
0.0127
0.0209
-0.0408
-0.0112
-0.0211
-0.0009
-0.0611
27.4732
40.5349
-62.7422
37
0.4599
0.5618
-0.1209
0
-0.2181
1.8459
-0.0025
0.0087
0.0161
0.0084
0.0044
0.0029
-0.0143
0.0119
-0.0019
0.0453
-0.1011
0.0129
-0.0453
0.013
-0.0184
34.0962
49.1629
-71.8211
38
0.377
0.0058
0.342
0.5368
-0.82
4.0551
-0.0125
-0.0771
0.0546
-0.0231
0.0111
0.0074
0.1191
0.0295
0.0013
0.0867
-0.0405
-0.0121
-0.0555
0.0417
-0.0568
32.1907
26.8543
-42.9735
39
0.1955
-0.184
-0.0344
1.012
0.2928
3.0171
-0.0124
-0.0085
-0.0615
-0.014
0.0006
-0.0085
0.0652
0.0756
0.0119
0.1006
0.0167
0.0366
0.0142
-0.0095
-0.0692
37.759
24.0871
-41.4945
40
0.0654
-0.2312
-0.5908
0.1185
0.2217
0.3592
-0.0025
0.0071
0.014
-0.0017
0.0035
-0.009
-0.0044
0.0051
-0.001
0.0134
0.0292
0.0515
0.042
0.0155
-0.0325
46.0969
27.0994
-43.9368
41
0.0053
1.5574
-0.8513
2.0684
-2.151
2.7278
-0.0166
-0.0498
0.0099
-0.008
0.0246
0.0175
0.061
0.0166
-0.008
0.0954
-0.0403
-0.0343
-0.0198
0.0298
-0.1102
33.2634
28.6155
-36.8773
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
{ A|2 - A|12 }
2
X-RAY DIFFRACTION
2
{ A|13 - A|77 }
3
X-RAY DIFFRACTION
3
{ A|78 - A|115 }
4
X-RAY DIFFRACTION
4
{ A|116 - A|127 }
5
X-RAY DIFFRACTION
5
{ A|128 - A|170 }
6
X-RAY DIFFRACTION
6
{ B|2 - B|12 }
7
X-RAY DIFFRACTION
7
{ B|13 - B|79 }
8
X-RAY DIFFRACTION
8
{ B|80 - B|117 }
9
X-RAY DIFFRACTION
9
{ B|118 - B|127 }
10
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