Domain of unknown function DUF4986 / Domain of unknown function DUF6805 / Domain of unknown function / Family of unknown function (DUF6805) / Beta-L-arabinofuranosidase, GH127 / Beta-L-arabinofuranosidase, GH127 catalytic domain / Six-hairpin glycosidase superfamily Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interest
Y
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.49 Å3/Da / Density % sol: 50.6 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 15-17% PEG 3350, MES pH 6.25-6.5, 0.2M ammonium formate, seeding from similar conditions
-
Data collection
Diffraction
Mean temperature: 100 K / Serial crystal experiment: N
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→55.899 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.945 / SU B: 17.765 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.397 / ESU R Free: 0.233 Details: Hydrogens have been added in their riding positions
Rfactor
Num. reflection
% reflection
Rfree
0.2208
3622
5.032 %
Rwork
0.1896
68360
-
all
0.191
-
-
obs
-
71982
99.963 %
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: 61.794 Å2
Baniso -1
Baniso -2
Baniso -3
1-
3.914 Å2
0 Å2
0 Å2
2-
-
-1.045 Å2
0 Å2
3-
-
-
-2.868 Å2
Refinement step
Cycle: LAST / Resolution: 2.4→55.899 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
12421
0
22
312
12755
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.005
0.012
12756
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.016
11763
X-RAY DIFFRACTION
r_angle_refined_deg
1.259
1.671
17292
X-RAY DIFFRACTION
r_angle_other_deg
0.492
1.588
27084
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.085
5
1542
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
6.964
5
80
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.437
10
2149
X-RAY DIFFRACTION
r_dihedral_angle_6_deg
15.086
10
627
X-RAY DIFFRACTION
r_chiral_restr
0.062
0.2
1856
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
15126
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
3030
X-RAY DIFFRACTION
r_nbd_refined
0.183
0.2
2128
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.153
0.2
10314
X-RAY DIFFRACTION
r_nbtor_refined
0.163
0.2
6027
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.067
0.2
6486
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.114
0.2
476
X-RAY DIFFRACTION
r_metal_ion_refined
0.134
0.2
5
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.148
0.2
16
X-RAY DIFFRACTION
r_nbd_other
0.144
0.2
39
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.18
0.2
12
X-RAY DIFFRACTION
r_mcbond_it
2.016
3.774
6183
X-RAY DIFFRACTION
r_mcbond_other
2.016
3.774
6183
X-RAY DIFFRACTION
r_mcangle_it
3.134
6.799
7720
X-RAY DIFFRACTION
r_mcangle_other
3.134
6.799
7721
X-RAY DIFFRACTION
r_scbond_it
2.31
3.978
6573
X-RAY DIFFRACTION
r_scbond_other
2.309
3.978
6574
X-RAY DIFFRACTION
r_scangle_it
3.742
7.215
9569
X-RAY DIFFRACTION
r_scangle_other
3.741
7.215
9570
X-RAY DIFFRACTION
r_lrange_it
6.057
45.559
54157
X-RAY DIFFRACTION
r_lrange_other
6.052
45.548
54044
X-RAY DIFFRACTION
r_ncsr_local_group_1
0.064
0.05
26238
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
0.06414
0.0501
1
2
A
X-RAY DIFFRACTION
Localncs
0.06414
0.0501
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
2.4-2.462
0.348
282
0.279
4954
0.282
5238
0.925
0.945
99.9618
0.251
2.462-2.53
0.272
250
0.27
4876
0.27
5128
0.952
0.951
99.961
0.239
2.53-2.603
0.264
248
0.248
4732
0.249
4980
0.955
0.961
100
0.216
2.603-2.683
0.277
234
0.24
4607
0.242
4841
0.953
0.966
100
0.209
2.683-2.77
0.295
274
0.231
4416
0.235
4690
0.951
0.969
100
0.197
2.77-2.867
0.264
261
0.216
4287
0.218
4548
0.959
0.972
100
0.183
2.867-2.975
0.264
218
0.212
4170
0.215
4388
0.959
0.973
100
0.185
2.975-3.096
0.231
217
0.216
4022
0.217
4239
0.963
0.97
100
0.19
3.096-3.234
0.274
168
0.22
3919
0.222
4087
0.951
0.969
100
0.199
3.234-3.391
0.26
196
0.21
3681
0.212
3877
0.96
0.973
100
0.191
3.391-3.574
0.203
186
0.21
3543
0.209
3729
0.977
0.977
100
0.195
3.574-3.79
0.238
172
0.191
3348
0.193
3522
0.967
0.981
99.9432
0.176
3.79-4.05
0.204
154
0.162
3155
0.164
3309
0.977
0.985
100
0.149
4.05-4.372
0.184
157
0.147
2936
0.149
3093
0.981
0.987
100
0.135
4.372-4.787
0.161
153
0.132
2720
0.133
2873
0.984
0.99
100
0.123
4.787-5.347
0.188
150
0.147
2454
0.15
2606
0.98
0.988
99.9233
0.138
5.347-6.165
0.218
114
0.18
2217
0.182
2332
0.973
0.984
99.9571
0.167
6.165-7.527
0.208
79
0.177
1892
0.179
1982
0.976
0.981
99.445
0.168
7.527-10.55
0.146
73
0.138
1507
0.138
1580
0.986
0.988
100
0.133
10.55-55.899
0.196
36
0.246
923
0.244
959
0.972
0.924
100
0.236
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
1.0543
-0.2229
0.1065
1.7918
0.9875
2.2359
0.0055
0.1408
-0.0765
-0.2377
-0.2848
0.2315
-0.0256
-0.2969
0.2793
0.0578
0.0124
-0.016
0.0802
-0.0596
0.0486
-8.2895
-36.8988
21.6665
2
1.9459
0.2501
0.6386
1.1886
0.4983
1.7833
-0.1271
0.2189
0.2413
-0.218
-0.0025
-0.041
-0.1341
-0.0129
0.1296
0.0855
-0.0274
-0.0102
0.1011
-0.0557
0.1553
-37.3928
-71.2696
29.0003
Refinement TLS group
Selection: ALL
+
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