Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Compound details
The crystallized sequence is: ...The crystallized sequence is: GSHMSAVNNAYDALIIEARKGNTQPALSWFALKSALSNNQIADWLQIALWAGQDKQVITVYNRYRHQQLPARGYAAVAVA YRNLQQWQNSLTLWQKALSLEPQNKDYQRGQILTLADAGHYDTALVKLKQLNSGAPDKANLLAEAYIYKLAGRHQDELRA MTESLPENASTQQYPTEYVQALRNNQLAAAIDDANLTPDIRADIHAELVRLSFMPTRSESERYAIADRALAQYAALEILW HDNPDRTAQYQRIQVDHLGALLTRDRYKDVISHYQRLKKTGQIIPPWGQYWVASAYLKDHQPKKAQSIMTELFYHKETIA PDLSDEELADLFYSHLESEN. As per the authors, the protein must have cleaved and only the C-terminal fragment crystallized. They do not know exactly at which residue the cleavage occurred.
Has ligand of interest
N
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.85 Å3/Da / Density % sol: 61.95 %
Crystal grow
Temperature: 300 K / Method: vapor diffusion, hanging drop Details: 15% w/v PEG 8000, 0.1 M Tris pH 7.1, 200 mM MgCl2, and 3% w/v cadaverine
-
Data collection
Diffraction
Mean temperature: 100 K / Serial crystal experiment: N
Method to determine structure: SAD / Resolution: 2.85→20.001 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.878 / SU B: 41.677 / SU ML: 0.344 / Cross valid method: FREE R-VALUE / ESU R Free: 0.414 Details: Hydrogens have been added in their riding positions
Rfactor
Num. reflection
% reflection
Rfree
0.2643
499
5.967 %
Rwork
0.2347
7863
-
all
0.237
-
-
obs
-
8362
92.469 %
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parameters
Biso mean: 49.606 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.598 Å2
-0.799 Å2
-0 Å2
2-
-
-1.598 Å2
0 Å2
3-
-
-
5.184 Å2
Refinement step
Cycle: LAST / Resolution: 2.85→20.001 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2125
0
3
19
2147
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.007
0.013
2205
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.017
2034
X-RAY DIFFRACTION
r_angle_refined_deg
1.424
1.647
3000
X-RAY DIFFRACTION
r_angle_other_deg
1.231
1.582
4667
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.795
5
262
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
32.137
21.212
132
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
19.091
15
363
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
15.061
15
19
X-RAY DIFFRACTION
r_chiral_restr
0.06
0.2
286
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
2499
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
535
X-RAY DIFFRACTION
r_nbd_refined
0.226
0.2
523
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.2
0.2
1852
X-RAY DIFFRACTION
r_nbtor_refined
0.168
0.2
1051
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.084
0.2
1038
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.175
0.2
53
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.204
0.2
20
X-RAY DIFFRACTION
r_nbd_other
0.291
0.2
60
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.201
0.2
2
X-RAY DIFFRACTION
r_mcbond_it
1.395
2.666
1048
X-RAY DIFFRACTION
r_mcbond_other
1.391
2.663
1047
X-RAY DIFFRACTION
r_mcangle_it
2.475
3.987
1310
X-RAY DIFFRACTION
r_mcangle_other
2.474
3.991
1311
X-RAY DIFFRACTION
r_scbond_it
1.137
2.772
1156
X-RAY DIFFRACTION
r_scbond_other
1.137
2.775
1157
X-RAY DIFFRACTION
r_scangle_it
2.053
4.109
1689
X-RAY DIFFRACTION
r_scangle_other
2.053
4.111
1690
X-RAY DIFFRACTION
r_lrange_it
4.794
29.988
2544
X-RAY DIFFRACTION
r_lrange_other
4.794
30.011
2545
X-RAY DIFFRACTION
r_ncsr_local_group_1
0.131
0.05
3782
Refine LS restraints NCS
Ens-ID
Dom-ID
Auth asym-ID
Refine-ID
Type
Rms dev position (Å)
Weight position
1
1
AAA
X-RAY DIFFRACTION
Localncs
0.13127
0.05007
1
2
BBB
X-RAY DIFFRACTION
Localncs
0.13127
0.05007
LS refinement shell
Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Rfactor all
Num. reflection all
Fsc free
Fsc work
% reflection obs (%)
WRfactor Rwork
2.85-2.922
0.207
11
0.277
236
0.274
666
0.852
0.767
37.0871
0.259
2.922-3.001
0.341
20
0.318
381
0.319
624
0.857
0.788
64.2628
0.259
3.001-3.086
0.33
38
0.344
588
0.343
627
0.741
0.803
99.8405
0.258
3.086-3.178
0.255
36
0.319
561
0.315
598
0.83
0.848
99.8328
0.231
3.178-3.28
0.329
37
0.276
542
0.279
580
0.825
0.877
99.8276
0.207
3.28-3.392
0.287
34
0.265
535
0.266
569
0.875
0.885
100
0.2
3.392-3.516
0.282
35
0.256
514
0.257
549
0.884
0.887
100
0.219
3.516-3.655
0.311
30
0.252
492
0.255
522
0.877
0.899
100
0.196
3.655-3.811
0.268
32
0.226
480
0.229
512
0.904
0.914
100
0.186
3.811-3.99
0.309
32
0.223
443
0.229
475
0.882
0.919
100
0.186
3.99-4.197
0.237
23
0.215
435
0.216
459
0.938
0.933
99.7821
0.18
4.197-4.439
0.309
28
0.181
416
0.188
444
0.908
0.952
100
0.156
4.439-4.729
0.212
25
0.179
394
0.181
419
0.955
0.961
100
0.159
4.729-5.084
0.17
26
0.212
360
0.209
386
0.973
0.948
100
0.199
5.084-5.534
0.32
24
0.233
342
0.239
366
0.922
0.937
100
0.209
5.534-6.129
0.203
15
0.215
305
0.214
320
0.958
0.937
100
0.192
6.129-6.969
0.172
17
0.207
280
0.205
297
0.957
0.949
100
0.195
6.969-8.287
0.247
15
0.184
226
0.188
241
0.962
0.965
100
0.189
8.287-10.827
0.217
13
0.18
195
0.182
209
0.968
0.978
99.5215
0.182
10.827-20.001
0.335
8
0.264
137
0.268
147
0.876
0.946
98.6395
0.283
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
1.3353
0.2058
1.2802
0.2438
-0.0867
1.9893
0.0751
-0.1602
0.0225
-0.0637
-0.0022
0.0607
-0.1688
-0.1733
-0.0729
0.391
0.1359
0.0131
0.4226
0.0369
0.02
4.421
34.288
52.696
2
2.6314
-0.322
1.7147
2.2587
-0.2424
3.2472
0.0972
-0.2396
0.2161
0.067
-0.134
0.2208
-0.1371
-0.134
0.0368
0.2118
0.0415
0.0814
0.3467
-0.0033
0.0816
2.625
34.163
82.92
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
ALL
AAA
224 - 359
2
X-RAY DIFFRACTION
2
ALL
BBB
220 - 343
+
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