protein catabolic process in the vacuole / GID complex / protein targeting to vacuole / negative regulation of gluconeogenesis / ubiquitin ligase complex / ubiquitin protein ligase activity / proteasome-mediated ubiquitin-dependent protein catabolic process Similarity search - Function
Resolution: 1.6→36.403 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.208 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.097 Details: Hydrogens have been added in their riding positions
Rfactor
Num. reflection
% reflection
Rfree
0.2197
1049
4.956 %
Rwork
0.1856
20116
-
all
0.187
-
-
obs
-
21165
96.481 %
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parameters
Biso mean: 21.394 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.735 Å2
0 Å2
-0.739 Å2
2-
-
-0.593 Å2
0 Å2
3-
-
-
0.065 Å2
Refinement step
Cycle: LAST / Resolution: 1.6→36.403 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1353
0
13
50
1416
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.01
0.013
1446
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.017
1236
X-RAY DIFFRACTION
r_angle_refined_deg
1.67
1.638
1968
X-RAY DIFFRACTION
r_angle_other_deg
1.458
1.578
2866
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.805
5
177
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.43
23.377
77
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.812
15
225
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
24.686
15
4
X-RAY DIFFRACTION
r_chiral_restr
0.084
0.2
176
X-RAY DIFFRACTION
r_gen_planes_refined
0.01
0.02
1651
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
346
X-RAY DIFFRACTION
r_nbd_refined
0.223
0.2
260
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.194
0.2
1114
X-RAY DIFFRACTION
r_nbtor_refined
0.184
0.2
679
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.083
0.2
641
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.12
0.2
48
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.141
0.2
7
X-RAY DIFFRACTION
r_nbd_other
0.142
0.2
29
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.116
0.2
4
X-RAY DIFFRACTION
r_mcbond_it
1.985
2.226
677
X-RAY DIFFRACTION
r_mcbond_other
1.984
2.226
677
X-RAY DIFFRACTION
r_mcangle_it
2.998
3.325
845
X-RAY DIFFRACTION
r_mcangle_other
2.997
3.328
846
X-RAY DIFFRACTION
r_scbond_it
2.576
2.401
769
X-RAY DIFFRACTION
r_scbond_other
2.575
2.403
770
X-RAY DIFFRACTION
r_scangle_it
3.836
3.524
1117
X-RAY DIFFRACTION
r_scangle_other
3.835
3.526
1118
X-RAY DIFFRACTION
r_lrange_it
5.03
24.55
1619
X-RAY DIFFRACTION
r_lrange_other
5.015
24.398
1606
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
1.6-1.642
0.249
44
0.29
1157
0.288
1596
0.809
0.785
75.2506
0.275
1.642-1.686
0.273
68
0.262
1280
0.262
1582
0.789
0.817
85.2086
0.238
1.686-1.735
0.278
87
0.243
1362
0.245
1515
0.835
0.849
95.6436
0.22
1.735-1.789
0.262
75
0.225
1400
0.227
1486
0.888
0.874
99.2598
0.197
1.789-1.847
0.28
71
0.209
1355
0.212
1430
0.881
0.908
99.7203
0.181
1.847-1.912
0.247
72
0.185
1316
0.188
1392
0.92
0.933
99.7126
0.16
1.912-1.984
0.176
67
0.175
1255
0.175
1331
0.937
0.943
99.3238
0.154
1.984-2.064
0.217
71
0.185
1225
0.187
1300
0.926
0.938
99.6923
0.164
2.064-2.156
0.252
55
0.19
1185
0.193
1245
0.917
0.937
99.5984
0.171
2.156-2.261
0.227
52
0.177
1126
0.179
1181
0.938
0.947
99.746
0.157
2.261-2.382
0.157
47
0.17
1085
0.169
1136
0.963
0.954
99.6479
0.155
2.382-2.526
0.189
52
0.174
1008
0.174
1064
0.951
0.952
99.6241
0.163
2.526-2.7
0.268
50
0.189
970
0.193
1021
0.925
0.946
99.9021
0.177
2.7-2.915
0.214
52
0.182
884
0.184
940
0.942
0.946
99.5745
0.177
2.915-3.191
0.239
51
0.174
816
0.177
872
0.946
0.954
99.4266
0.178
3.191-3.564
0.274
36
0.177
745
0.18
787
0.927
0.96
99.2376
0.186
3.564-4.109
0.178
44
0.154
668
0.156
715
0.954
0.966
99.5804
0.17
4.109-5.016
0.157
26
0.146
558
0.146
587
0.972
0.972
99.4889
0.172
5.016-7.028
0.217
24
0.221
448
0.221
475
0.939
0.947
99.3684
0.245
7.028-36.403
0.335
5
0.253
273
0.254
280
0.903
0.924
99.2857
0.308
+
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