Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 20 - 123 / Label seq-ID: 20 - 123
Dom-ID
Component-ID
Ens-ID
1
1
1
2
1
1
3
2
2
4
2
2
5
3
3
6
3
3
NCS ensembles :
ID
Details
1
LocalNCSretraintsbetweendomains: 12
2
LocalNCSretraintsbetweendomains: 34
3
LocalNCSretraintsbetweendomains: 56
-
Components
#1: Protein
Cereblonisoform4
Mass: 13632.500 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Magnetospirillum gryphiswaldense (magnetotactic) Gene: MGR_0879 / Production host: Escherichia coli (E. coli) / References: UniProt: A4TVL0
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→47.554 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.622 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.108 Details: Hydrogens have been added in their riding positions
Rfactor
Num. reflection
% reflection
Rfree
0.2237
1676
5.008 %
Rwork
0.1762
31789
-
all
0.179
-
-
obs
-
33465
99.985 %
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: 37.081 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.229 Å2
0 Å2
-0 Å2
2-
-
0.488 Å2
-0 Å2
3-
-
-
-0.259 Å2
Refinement step
Cycle: LAST / Resolution: 1.7→47.554 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2295
0
63
85
2443
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.015
0.011
2466
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.016
2154
X-RAY DIFFRACTION
r_angle_refined_deg
1.809
1.632
3355
X-RAY DIFFRACTION
r_angle_other_deg
0.653
1.569
4916
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.313
5
306
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
10.029
7.5
30
X-RAY DIFFRACTION
r_dihedral_angle_other_2_deg
0.218
10
3
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.567
10
314
X-RAY DIFFRACTION
r_dihedral_angle_6_deg
18.739
10
103
X-RAY DIFFRACTION
r_chiral_restr
0.11
0.2
329
X-RAY DIFFRACTION
r_gen_planes_refined
0.014
0.02
2971
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
669
X-RAY DIFFRACTION
r_nbd_refined
0.192
0.2
336
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.211
0.2
1855
X-RAY DIFFRACTION
r_nbtor_refined
0.193
0.2
1152
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.088
0.2
1248
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.129
0.2
65
X-RAY DIFFRACTION
r_metal_ion_refined
0.11
0.2
12
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.152
0.2
18
X-RAY DIFFRACTION
r_nbd_other
0.218
0.2
71
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.082
0.2
9
X-RAY DIFFRACTION
r_mcbond_it
4.781
3.779
1212
X-RAY DIFFRACTION
r_mcbond_other
4.782
3.779
1212
X-RAY DIFFRACTION
r_mcangle_it
5.838
6.737
1510
X-RAY DIFFRACTION
r_mcangle_other
5.836
6.74
1511
X-RAY DIFFRACTION
r_scbond_it
6.093
4.226
1254
X-RAY DIFFRACTION
r_scbond_other
6.091
4.227
1255
X-RAY DIFFRACTION
r_scangle_it
8.346
7.54
1841
X-RAY DIFFRACTION
r_scangle_other
8.344
7.54
1842
X-RAY DIFFRACTION
r_lrange_it
9.901
42.119
2656
X-RAY DIFFRACTION
r_lrange_other
9.9
41.965
2651
X-RAY DIFFRACTION
r_ncsr_local_group_1
0.124
0.05
3043
X-RAY DIFFRACTION
r_ncsr_local_group_2
0.115
0.05
2427
X-RAY DIFFRACTION
r_ncsr_local_group_3
0.123
0.05
2421
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
0.12434
0.05008
1
2
A
X-RAY DIFFRACTION
Localncs
0.12434
0.05008
2
3
A
X-RAY DIFFRACTION
Localncs
0.11533
0.05007
2
4
A
X-RAY DIFFRACTION
Localncs
0.11533
0.05007
3
5
A
X-RAY DIFFRACTION
Localncs
0.12308
0.05007
3
6
A
X-RAY DIFFRACTION
Localncs
0.12308
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
1.7-1.744
0.331
124
0.333
2326
0.333
2450
0.838
0.821
100
0.335
1.744-1.792
0.302
116
0.272
2218
0.274
2334
0.925
0.939
100
0.26
1.792-1.844
0.274
115
0.236
2191
0.238
2306
0.942
0.958
100
0.214
1.844-1.9
0.256
114
0.211
2151
0.213
2265
0.956
0.969
100
0.185
1.9-1.963
0.249
112
0.193
2059
0.196
2171
0.963
0.974
100
0.165
1.963-2.031
0.216
103
0.166
2011
0.168
2114
0.972
0.981
100
0.14
2.031-2.108
0.188
104
0.156
1942
0.158
2046
0.977
0.984
100
0.132
2.108-2.194
0.19
99
0.149
1859
0.151
1958
0.978
0.986
100
0.127
2.194-2.291
0.174
92
0.136
1804
0.138
1896
0.982
0.988
100
0.117
2.291-2.403
0.196
90
0.141
1727
0.144
1817
0.976
0.988
100
0.124
2.403-2.532
0.211
86
0.169
1622
0.172
1708
0.974
0.984
100
0.151
2.532-2.685
0.239
83
0.181
1572
0.184
1655
0.965
0.981
100
0.165
2.685-2.87
0.2
77
0.166
1469
0.167
1546
0.978
0.983
100
0.156
2.87-3.099
0.215
74
0.16
1363
0.162
1437
0.968
0.983
100
0.157
3.099-3.393
0.219
66
0.167
1266
0.17
1332
0.971
0.983
100
0.176
3.393-3.792
0.192
60
0.163
1156
0.165
1216
0.979
0.984
100
0.176
3.792-4.374
0.172
55
0.153
1035
0.153
1090
0.98
0.986
100
0.173
4.374-5.345
0.269
46
0.161
879
0.166
926
0.969
0.984
99.892
0.191
5.345-7.512
0.3
37
0.245
712
0.248
750
0.957
0.966
99.8667
0.285
7.512-47.554
0.29
23
0.233
422
0.235
447
0.957
0.964
99.5526
0.284
+
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