Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal grow
Temperature: 293.1 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 2.1 M AMMONIUM SULPHATE, 2% PEG 400, 0.1 M NA HEPES PH 7.2.PRIOR TO SETTING UP CRYSTALLIZATION PLATES, CHYMOTRYPSIN WAS ADDED TO THE PROTEIN SAMPLE TO A FINAL CONCENTRATION OF 0.57 ...Details: 2.1 M AMMONIUM SULPHATE, 2% PEG 400, 0.1 M NA HEPES PH 7.2.PRIOR TO SETTING UP CRYSTALLIZATION PLATES, CHYMOTRYPSIN WAS ADDED TO THE PROTEIN SAMPLE TO A FINAL CONCENTRATION OF 0.57 MICROMOLAR., VAPOR DIFFUSION, HANGING DROP, temperature 293.1K
Resolution: 2.4→30.44 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.941 / SU B: 19.095 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.435 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23463
705
5 %
RANDOM
Rwork
0.19961
-
-
-
obs
0.2015
13463
99.93 %
-
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: 54.789 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.55 Å2
0 Å2
0 Å2
2-
-
2.55 Å2
0 Å2
3-
-
-
-3.1 Å2
Refinement step
Cycle: LAST / Resolution: 2.4→30.44 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2527
0
1
34
2562
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.014
0.022
2577
X-RAY DIFFRACTION
r_angle_refined_deg
1.392
1.955
3482
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.578
5
317
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
41.759
23.796
108
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
20.25
15
464
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
20.398
15
14
X-RAY DIFFRACTION
r_chiral_restr
0.093
0.2
396
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.021
1895
X-RAY DIFFRACTION
r_mcbond_it
0.561
1.5
1589
X-RAY DIFFRACTION
r_mcangle_it
1.038
2
2562
X-RAY DIFFRACTION
r_scbond_it
1.756
3
988
X-RAY DIFFRACTION
r_scangle_it
2.817
4.5
920
LS refinement shell
Resolution: 2.4→2.462 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.322
58
-
Rwork
0.247
948
-
obs
-
-
99.6 %
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
16.4253
-2.4869
-5.7861
0.5241
0.0086
8.0853
-0.0518
-0.1089
1.2173
0.07
0.0843
-0.2362
-0.5192
0.3854
-0.0325
0.3326
-0.0606
-0.0149
0.4263
0.0347
0.3649
5.8004
6.8826
-25.1736
2
15.3432
8.2844
3.4993
22.3563
12.9645
7.6647
-0.2605
0.0204
0.2535
-0.144
0.1782
0.1513
-0.1123
0.0654
0.0824
0.4251
0.1224
0.0023
0.3083
0.0414
0.1751
0.0779
5.7011
-19.0493
3
26.029
-2.7731
8.1221
8.6929
-6.1025
22.6285
-0.2347
-0.1308
1.0893
0.4474
0.353
0.8999
-0.5815
-0.7965
-0.1182
0.2035
0.0085
0.0819
0.2339
0.0271
0.1809
-5.8838
2.3769
-21.2212
4
8.2769
-5.7082
4.4652
5.5636
-6.8161
10.995
-0.2448
-0.4776
-0.06
0.2598
0.4641
0.1328
-0.3184
-0.5816
-0.2193
0.3078
-0.0179
0.081
0.3165
0.0176
0.2254
-5.5468
-0.1871
-13.1725
5
18.2636
18.7938
-10.0258
20.1994
-6.3054
24.5363
0.9391
-0.598
2.1065
1.0149
-0.7569
2.3332
-0.8182
-0.071
-0.1823
0.7262
0.0053
-0.1877
0.2453
-0.0253
0.4442
1.9472
0.1047
-8.7584
6
27.7124
-9.6454
7.3476
7.4158
-0.0291
12.4105
0.1014
-0.343
0.804
0.3617
0.2353
-0.3631
-1.0011
0.8215
-0.3367
0.3718
-0.1084
-0.0595
0.1072
-0.018
0.2505
7.8489
4.1986
-14.9107
7
5.0673
8.2117
-2.006
29.8622
-6.1259
4.9156
-0.2618
-0.0624
-0.1219
0.1996
0.0429
-0.8092
0.043
0.5281
0.2189
0.1809
-0.0072
-0.0726
0.2624
0.0267
0.156
8.5813
-5.1926
-17.2613
8
10.3594
-5.742
4.9298
7.4681
-1.8645
2.5668
0.0901
0.0883
-0.0227
0.3362
-0.0957
-0.0706
0.0441
0.1796
0.0056
0.3895
-0.131
-0.0526
0.5514
0.0536
0.1707
3.7047
-9.4223
-10.9978
9
4.4347
-2.2272
2.4053
1.8375
-0.8975
7.6956
-0.1028
-0.0164
-0.2503
0.0883
0.0811
0.2761
0.3681
-0.4739
0.0217
0.2075
-0.0457
0.0097
0.2253
0.0343
0.1817
-3.269
-9.5692
-17.9242
10
10.2551
1.6152
-2.6625
5.4374
0.8432
6.066
0.0803
0.2782
-0.3378
-0.3971
-0.034
-0.5064
0.2503
0.0465
-0.0462
0.17
-0.0108
-0.01
0.1942
0.03
0.1882
4.6168
-4.111
-25.9629
11
7.3466
-6.0548
7.6233
7.1467
-2.1724
15.7703
-0.144
-0.6679
-0.2503
0.1722
0.1875
0.356
-0.0592
-1.3814
-0.0434
0.1086
-0.0188
0.0677
0.4806
0.1202
0.2252
-12.3941
-0.6498
-30.3665
12
6.9078
3.3878
4.6393
12.0676
-2.6094
5.4539
0.0702
-0.7299
0.1894
0.7123
-0.0428
0.2204
-0.235
-0.7176
-0.0275
0.2258
0.0718
0.0011
0.342
0.0646
0.2042
-6.866
3.192
-31.6881
13
3.5885
-1.6653
-0.509
6.0911
5.7868
16.7686
-0.0925
-0.2811
0.525
0.1663
0.2606
-0.2766
-1.1731
-0.1432
-0.1681
0.2766
0.0275
0.0245
0.2197
-0.0032
0.2609
-2.4006
6.8667
-36.3007
14
0.4521
-0.3856
-2.2199
10.244
-1.3127
11.9705
0.1338
0.1336
0.0277
-0.1948
0.0835
0.3504
-0.6191
-0.7956
-0.2172
0.2151
0.0236
-0.0133
0.3197
0.0643
0.2474
-8.7907
3.8666
-44.1759
15
7.4478
0.7752
-7.2729
0.9296
2.9974
23.7294
-0.569
-0.0105
0.1264
-0.2885
-0.3683
0.2671
-0.4382
-1.7056
0.9373
0.2077
-0.0049
-0.082
0.5961
0.1384
0.2708
-13.2154
-2.1245
-40.8306
16
22.2365
5.1975
-14.8608
5.7622
-2.5286
10.1381
-0.2905
0.9342
-0.1334
-0.0603
0.1501
0.3347
0.2766
-0.6794
0.1404
0.5103
-0.2093
-0.2459
0.477
0.1118
0.2659
-9.9139
-8.6264
-38.1843
17
5.2332
7.4137
-0.9803
13.5607
-9.0899
19.7498
0.0303
0.124
-0.1421
-0.5431
-0.0337
-0.1651
1.4318
0.1985
0.0034
0.3656
0.1421
-0.0618
0.4658
-0.0928
0.2334
-0.1017
-6.9544
-44.3482
18
4.1054
-1.1557
2.417
4.2899
-1.5699
9.6865
0.029
0.2036
-0.1844
-0.322
-0.0889
-0.234
-0.0376
0.529
0.06
0.1884
0.0173
0.0212
0.2313
0.0318
0.1629
2.6378
-0.0196
-43.1756
19
3.7469
2.4035
-0.2867
9.3838
1.0061
15.1623
0.1097
0.2555
-0.2346
0.0141
-0.0489
-0.1914
0.6875
0.2628
-0.0609
0.1512
0.037
-0.01
0.2124
0.0344
0.1937
2.1617
-2.8047
-35.3454
20
10.1053
6.9602
0.6551
13.4016
-9.3286
11.1542
0.5508
0.103
-0.6568
-0.0879
0.2265
0.193
0.5697
-0.176
-0.7774
0.2946
-0.0381
-0.016
0.2741
-0.0154
0.283
-3.7165
-7.0821
-30.2894
21
61.2494
19.0652
-14.6885
29.0613
-4.3085
3.5257
0.0505
1.0939
0.3001
1.2816
0.0553
-0.2328
-0.0024
-0.2585
-0.1057
0.0951
0.1187
0.0095
0.6814
0.1039
0.2959
-26.6347
3.8444
-32.4002
22
3.7547
-4.0422
1.9671
27.0431
15.186
14.2439
-0.2105
0.2507
0.4901
-0.9024
0.1379
-0.8451
-1.0028
0.5335
0.0726
0.2166
-0.1416
-0.0594
0.5606
0.2519
0.3456
-31.743
9.4383
-31.5527
23
2.6192
5.7948
0.6634
14.9642
-0.1074
2.5036
-0.1705
-0.1238
0.4833
-0.2286
0.0341
0.1276
0.305
-0.0267
0.1364
0.2838
0.0652
-0.2689
0.6821
-0.1135
0.9379
-30.6231
4.9509
-24.2436
24
14.4932
-9.546
9.2753
14.2753
-1.4691
18.8425
0.3768
0.5199
0.8013
-0.0431
-0.5612
-0.4213
0.2558
1.1126
0.1844
0.34
0.1527
0.0027
0.5176
0.0821
0.3622
-27.9667
-2.8743
-24.4981
25
21.3689
-3.7867
4.7019
26.4265
20.2239
18.3626
0.1237
-0.1821
-2.013
-1.0354
1.3686
-1.0195
-0.7019
1.4423
-1.4923
0.3811
0.259
0.0927
1.2154
0.2664
0.5663
-24.5815
-4.6186
-32.8304
26
38.2577
-2.16
-7.6761
1.0875
4.9674
22.8885
-1.4233
2.9577
-0.4801
0.1528
0.0778
0.2867
0.7774
0.3898
1.3455
0.5981
0.0875
0.0552
0.4385
0.0707
0.5703
-33.0857
-7.3672
-34.3166
27
17.0849
16.8863
13.5216
49.8507
-2.3899
18.2027
0.8588
0.5999
-0.8519
-0.2342
-0.383
-1.2361
1.2911
0.988
-0.4759
0.5416
0.2209
0.0444
0.3933
0.0687
0.3125
-36.5533
-6.2932
-26.3446
28
9.627
4.0399
-6.4029
1.8486
-3.5403
9.0407
0.1334
-0.5357
-0.273
-0.0777
-0.1621
-0.0949
0.6504
-0.193
0.0287
0.2219
0.0138
-0.0576
0.3232
0.0863
0.282
-41.6334
2.0607
-26.8834
29
12.4909
8.1236
6.4421
6.7137
9.0516
19.8947
-0.1507
-0.9214
0.3084
-0.0078
-0.5121
0.3559
0.2666
-0.0033
0.6627
0.2068
0.1276
-0.0129
0.3948
0.0588
0.2639
-39.7592
2.9693
-35.2507
30
3.1898
-1.4235
-0.4343
0.6976
-0.8444
19.8335
0.3119
0.3623
-0.791
-0.1205
-0.1068
0.3671
0.0371
1.2396
-0.2051
0.4864
0.2135
0.0242
0.865
0.0173
0.6706
-33.4098
-1.1984
-40.4952
31
3.9578
3.2779
-2.0017
2.722
-1.6492
1.0289
-0.3479
0.3868
-0.0401
-0.3423
0.3086
0.006
0.0887
-0.2267
0.0393
0.5274
0.0842
-0.1277
0.389
-0.047
0.3584
-20.9399
-13.8351
-12.4298
32
9.8268
4.96
-0.563
10.2634
-0.1913
22.8998
-0.1556
0.4602
0.2638
-0.2347
-0.1541
1.0413
-0.054
-0.9606
0.3097
0.1768
0.025
-0.012
0.2344
-0.0027
0.3106
-24.1477
-18.2357
-5.699
33
6.0657
0.661
0.8255
11.6032
-0.3821
5.8659
-0.0874
0.0557
0.1699
0.1465
0.0011
0.8063
-0.3135
-0.2145
0.0863
0.1515
0.0119
0.0609
0.1939
-0.0225
0.2415
-21.7541
-12.9894
1.4693
34
3.572
1.3836
-0.3753
10.2955
3.2509
7.6395
0.1213
0.0081
0.3496
-0.5647
0.0599
-0.0652
-0.3749
0.7024
-0.1811
0.2948
0.0095
0.0125
0.2443
0.0402
0.2426
-14.933
-7.4572
-2.4329
35
32.9117
-7.9337
-5.6776
6.4522
-5.719
12.0481
0.0152
0.7032
-0.6333
0.0433
-0.3094
0.0373
-0.1074
0.1264
0.2941
0.4906
-0.1345
0.0793
0.2362
-0.0253
0.1116
-12.5733
-11.3467
-9.4797
36
9.9866
-5.9242
-8.4738
9.1505
7.8851
21.0461
0.0501
-0.0219
0.1154
0.3604
0.0994
-0.7787
0.2434
1.2323
-0.1495
0.1256
0.0597
-0.0305
0.4761
-0.0317
0.4032
-7.8894
-17.3168
-1.8824
37
6.5277
3.142
-4.0179
9.6962
2.2991
4.6653
-0.1488
-0.864
-0.2259
0.5397
-0.0346
-0.0398
0.3853
0.745
0.1834
0.2968
0.0373
-0.0282
0.4248
0.0175
0.2229
-13.2071
-16.7894
5.3836
38
4.3875
8.1957
-3.8535
15.6099
-5.5796
16.2218
-0.0392
-0.1673
-0.3824
0.1466
-0.1652
-0.5601
0.5002
0.0687
0.2044
0.5219
0.2292
0.3437
0.3175
0.2096
0.3994
-18.1114
-24.8089
4.8144
39
7.4286
-0.9578
-5.9689
4.3797
-1.0696
30.9709
-0.0351
0.197
-0.491
-0.07
-0.1555
0.2319
0.6452
0.2089
0.1907
0.1949
0.0137
0.0366
0.1599
-0.0128
0.2311
-15.8068
-23.6161
-6.0872
40
8.9379
-11.9667
-1.0483
17.5678
-3.0119
20.5466
0.598
0.3535
0.6957
-1.007
-0.5096
-1.0762
-0.2201
0.262
-0.0884
0.2543
-0.0928
-0.0123
0.3224
0.0226
0.2522
-10.1713
-20.3657
-14.728
41
2.9005
-3.5743
-1.0792
4.8579
0.2773
16.6632
0.611
0.5005
-0.2218
-0.7931
-0.1558
0.4725
0.7225
-0.2301
-0.4552
0.3186
-0.0044
0.019
0.6784
0.0148
0.3151
-25.937
-1.783
-15.837
42
10.7875
-3.5295
-0.4334
2.2089
-4.1064
17.1925
0.4607
0.1591
-0.5509
-0.1643
0.0676
0.2947
0.0118
-0.4604
-0.5283
0.2472
0.0512
-0.0077
0.2336
-0.012
0.1938
-24.5052
-1.9989
-7.8664
43
5.0407
1.8341
1.3605
11.4874
-4.7755
5.4941
0.4421
0.4101
-0.04
-0.125
-0.0417
0.6223
-0.2994
-0.6552
-0.4004
0.3232
0.1311
0.1158
0.3952
-0.0296
0.2401
-28.0553
3.7534
-2.9534
44
13.7993
3.305
-7.2118
7.9784
-0.1205
4.1283
0.1854
0.1931
1.1233
-0.6356
0.2154
1.1656
-0.2526
-0.0595
-0.4008
0.613
0.218
0.0985
0.3222
0.1122
0.4118
-27.8647
11.061
-7.6236
45
23.5407
10.8971
4.4151
25.672
10.9269
16.5742
-0.3125
1.4421
0.6408
-1.7695
0.5794
0.3537
-2.365
-0.0866
-0.2669
0.4712
0.0128
0.1679
0.3422
0.0322
0.1602
-22.9565
8.7792
-15.2272
46
5.9909
-6.43
-3.392
15.0126
0.9284
13.216
-0.0548
0.389
0.184
0.0856
-0.4338
-0.1755
-0.06
0.6177
0.4886
0.408
-0.1516
0.1841
0.2165
0.1211
0.4949
-16.0608
12.1138
-7.363
47
18.2983
-8.6791
4.0919
16.243
-16.9605
19.5401
0.4774
-0.1474
0.0935
1.5047
-0.1468
0.2565
-2.1429
0.2084
-0.3306
0.8962
0.0578
0.151
0.114
-0.0967
0.3667
-21.3901
12.637
-0.4761
48
1.2795
3.274
-3.5582
9.1329
-6.504
20.7131
0.0261
-0.1547
0.0238
0.109
-0.0322
-0.1074
-0.3193
1.3407
0.0062
0.2872
-0.0572
0.0301
0.4527
-0.1959
0.414
-17.1113
4.7824
2.5351
49
0.5709
-0.4246
-1.6088
10.6793
-7.7641
12.3279
0.062
-0.2928
0.27
0.4918
0.2044
-0.8032
-0.4826
0.8542
-0.2665
0.3081
-0.028
-0.0238
0.3697
-0.0696
0.3061
-15.3008
1.2524
-4.597
50
7.9132
-6.4587
0.3076
6.182
-4.6586
21.3691
-0.3371
0.3372
0.6282
0.1694
-0.2487
-0.6319
0.4143
-0.2744
0.5858
0.2685
-0.0082
0.1124
0.4327
0.016
0.2281
-14.0459
1.6658
-14.9247
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
911 - 916
2
X-RAY DIFFRACTION
2
A
917 - 921
3
X-RAY DIFFRACTION
3
A
922 - 926
4
X-RAY DIFFRACTION
4
A
927 - 932
5
X-RAY DIFFRACTION
5
A
933 - 938
6
X-RAY DIFFRACTION
6
A
939 - 943
7
X-RAY DIFFRACTION
7
A
944 - 951
8
X-RAY DIFFRACTION
8
A
952 - 956
9
X-RAY DIFFRACTION
9
A
957 - 967
10
X-RAY DIFFRACTION
10
A
968 - 974
11
X-RAY DIFFRACTION
11
B
912 - 919
12
X-RAY DIFFRACTION
12
B
920 - 925
13
X-RAY DIFFRACTION
13
B
926 - 930
14
X-RAY DIFFRACTION
14
B
931 - 936
15
X-RAY DIFFRACTION
15
B
937 - 942
16
X-RAY DIFFRACTION
16
B
943 - 948
17
X-RAY DIFFRACTION
17
B
949 - 954
18
X-RAY DIFFRACTION
18
B
955 - 963
19
X-RAY DIFFRACTION
19
B
964 - 968
20
X-RAY DIFFRACTION
20
B
969 - 974
21
X-RAY DIFFRACTION
21
C
907 - 912
22
X-RAY DIFFRACTION
22
C
913 - 917
23
X-RAY DIFFRACTION
23
C
918 - 922
24
X-RAY DIFFRACTION
24
C
923 - 928
25
X-RAY DIFFRACTION
25
C
929 - 933
26
X-RAY DIFFRACTION
26
C
934 - 941
27
X-RAY DIFFRACTION
27
C
942 - 947
28
X-RAY DIFFRACTION
28
C
948 - 954
29
X-RAY DIFFRACTION
29
C
955 - 959
30
X-RAY DIFFRACTION
30
C
960 - 965
31
X-RAY DIFFRACTION
31
D
903 - 910
32
X-RAY DIFFRACTION
32
D
911 - 918
33
X-RAY DIFFRACTION
33
D
919 - 925
34
X-RAY DIFFRACTION
34
D
926 - 932
35
X-RAY DIFFRACTION
35
D
933 - 937
36
X-RAY DIFFRACTION
36
D
938 - 942
37
X-RAY DIFFRACTION
37
D
943 - 950
38
X-RAY DIFFRACTION
38
D
951 - 956
39
X-RAY DIFFRACTION
39
D
957 - 965
40
X-RAY DIFFRACTION
40
D
966 - 970
41
X-RAY DIFFRACTION
41
E
903 - 910
42
X-RAY DIFFRACTION
42
E
911 - 917
43
X-RAY DIFFRACTION
43
E
918 - 923
44
X-RAY DIFFRACTION
44
E
924 - 929
45
X-RAY DIFFRACTION
45
E
930 - 937
46
X-RAY DIFFRACTION
46
E
938 - 945
47
X-RAY DIFFRACTION
47
E
946 - 950
48
X-RAY DIFFRACTION
48
E
951 - 956
49
X-RAY DIFFRACTION
49
E
957 - 961
50
X-RAY DIFFRACTION
50
E
962 - 968
+
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