Ens-ID: 1 / End auth comp-ID: ARG / End label comp-ID: ARG
Dom-ID
Component-ID
Beg auth comp-ID
Beg label comp-ID
Auth asym-ID
Label asym-ID
Auth seq-ID
Label seq-ID
1
1
LEU
LEU
A
A
190 - 1410
190 - 1410
2
2
SER
SER
B
B
41 - 1410
41 - 1410
NCS ensembles : (Details: Local NCS retraints between domains: 1 2)
-
Components
#1: Protein
GH92alpha-1,2-mannosidase
Mass: 155300.016 Da / Num. of mol.: 2 Fragment: The first CBM32 domain in subunit B is disordered and therefore residues B79 to B227 are missing from the model. Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neobacillus novalis (bacteria) / Production host: Bacillus subtilis (bacteria)
Mass: 18.015 Da / Num. of mol.: 561 / Source method: isolated from a natural source / Formula: H2O
Compound details
The first CBM32 domain in subunit B is disordered and therefore residues B79 to B227 are missing ...The first CBM32 domain in subunit B is disordered and therefore residues B79 to B227 are missing from the model.
Has ligand of interest
N
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.63 Å3/Da / Density % sol: 53.22 %
Crystal grow
Temperature: 290 K / Method: vapor diffusion, sitting drop Details: 21% PEG 3350, 0.1 M bis-Tris-propane pH 6.6, 0.2M sodium citrate, MMS
-
Data collection
Diffraction
Mean temperature: 100 K / Serial crystal experiment: N
Resolution: 2.29→47.923 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.917 / SU B: 10.034 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.307 / ESU R Free: 0.227 / Details: Hydrogens have not been used
Rfactor
Num. reflection
% reflection
Rfree
0.2458
6947
4.922 %
Rwork
0.2053
134197
-
all
0.207
-
-
obs
-
141144
97.987 %
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: 32.923 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.719 Å2
0 Å2
-4.093 Å2
2-
-
-0.854 Å2
-0 Å2
3-
-
-
-0.199 Å2
Refinement step
Cycle: LAST / Resolution: 2.29→47.923 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
20140
0
89
561
20790
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.008
0.012
20765
X-RAY DIFFRACTION
r_angle_refined_deg
1.533
1.639
28114
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.254
5
2592
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.222
24.06
1037
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.452
15
3311
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.692
15
71
X-RAY DIFFRACTION
r_chiral_restr
0.113
0.2
2710
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
15987
X-RAY DIFFRACTION
r_nbd_refined
0.216
0.2
9007
X-RAY DIFFRACTION
r_nbtor_refined
0.312
0.2
13994
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.13
0.2
943
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.161
0.2
43
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.203
0.2
10
X-RAY DIFFRACTION
r_mcbond_it
2.927
3.243
10407
X-RAY DIFFRACTION
r_mcangle_it
4.344
4.853
12966
X-RAY DIFFRACTION
r_scbond_it
3.548
3.345
10358
X-RAY DIFFRACTION
r_scangle_it
5.139
4.921
15148
X-RAY DIFFRACTION
r_lrange_it
9.701
42.296
30873
X-RAY DIFFRACTION
r_ncsr_local_group_1
0.069
0.05
40258
Refine LS restraints NCS
Ens-ID
Dom-ID
Auth asym-ID
Refine-ID
Type
Rms dev position (Å)
Weight position
1
1
A
X-RAY DIFFRACTION
Localncs
0.06899
0.05012
1
2
B
X-RAY DIFFRACTION
Localncs
0.06899
0.05012
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
2.29-2.349
0.353
506
0.332
10020
0.333
10597
0.536
0.562
99.33
0.328
2.349-2.414
0.335
479
0.315
9748
0.316
10317
0.662
0.68
99.1277
0.308
2.414-2.483
0.331
494
0.304
9492
0.305
10081
0.712
0.728
99.0576
0.296
2.483-2.56
0.351
457
0.282
9191
0.285
9757
0.746
0.775
98.8829
0.271
2.56-2.643
0.327
502
0.286
8775
0.288
9473
0.765
0.781
97.931
0.272
2.643-2.736
0.296
418
0.261
8477
0.263
9132
0.818
0.834
97.4047
0.247
2.736-2.839
0.287
425
0.256
8278
0.258
8853
0.844
0.848
98.3057
0.24
2.839-2.954
0.313
376
0.247
8071
0.25
8551
0.836
0.861
98.7838
0.233
2.954-3.085
0.278
408
0.229
7636
0.232
8153
0.871
0.889
98.6631
0.216
3.085-3.235
0.246
362
0.211
7314
0.212
7800
0.908
0.92
98.4103
0.2
3.235-3.409
0.273
305
0.209
6906
0.212
7399
0.895
0.927
97.4591
0.201
3.409-3.615
0.238
304
0.198
6495
0.199
7064
0.928
0.941
96.2486
0.193
3.615-3.863
0.238
344
0.179
6119
0.183
6607
0.935
0.951
97.8205
0.176
3.863-4.17
0.185
320
0.143
5735
0.145
6185
0.959
0.969
97.8981
0.142
4.17-4.564
0.163
296
0.125
5241
0.127
5686
0.967
0.974
97.3795
0.127
4.564-5.097
0.162
256
0.115
4683
0.118
5140
0.97
0.978
96.0895
0.117
5.097-5.875
0.195
248
0.142
4139
0.145
4566
0.958
0.969
96.0797
0.142
5.875-7.168
0.203
197
0.168
3563
0.17
3882
0.958
0.967
96.8573
0.168
7.168-10.026
0.185
157
0.142
2734
0.145
3018
0.967
0.976
95.7919
0.15
10.026-47.923
0.164
93
0.162
1581
0.162
1768
0.972
0.97
94.6833
0.174
+
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