: / Cip1-like, core domain / Domain of unknown function DUF1587 / Domain of unknown function DUF1588 / Domain of unknown function DUF1592 / Domain of unknown function DUF1595 / Protein of unknown function (DUF1587) / Protein of unknown function (DUF1588) / Protein of unknown function (DUF1592) / Protein of unknown function (DUF1595) ...: / Cip1-like, core domain / Domain of unknown function DUF1587 / Domain of unknown function DUF1588 / Domain of unknown function DUF1592 / Domain of unknown function DUF1595 / Protein of unknown function (DUF1587) / Protein of unknown function (DUF1588) / Protein of unknown function (DUF1592) / Protein of unknown function (DUF1595) / Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. Similarity search - Domain/homology
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→38.457 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.883 / SU B: 4.095 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.136 Details: Hydrogens have been addeed in their riding positions
Rfactor
Num. reflection
% reflection
Rfree
0.2404
1135
4.978 %
Rwork
0.195
21667
-
all
0.197
-
-
obs
-
22802
96.844 %
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: 12.22 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.158 Å2
-0.284 Å2
-0.748 Å2
2-
-
0.033 Å2
-0.832 Å2
3-
-
-
-0.113 Å2
Refinement step
Cycle: LAST / Resolution: 1.8→38.457 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1745
0
134
139
2018
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.01
0.012
1952
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.015
1674
X-RAY DIFFRACTION
r_angle_refined_deg
2.4
1.777
2677
X-RAY DIFFRACTION
r_angle_other_deg
0.54
1.646
3819
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.984
5
236
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
2.216
5
3
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.376
10
248
X-RAY DIFFRACTION
r_dihedral_angle_6_deg
14.173
10
82
X-RAY DIFFRACTION
r_chiral_restr
0.062
0.2
269
X-RAY DIFFRACTION
r_gen_planes_refined
0.01
0.02
2356
X-RAY DIFFRACTION
r_gen_planes_other
0.011
0.02
438
X-RAY DIFFRACTION
r_nbd_refined
0.332
0.2
499
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.203
0.2
1565
X-RAY DIFFRACTION
r_nbtor_refined
0.175
0.2
981
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.074
0.2
968
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.155
0.2
125
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.072
0.2
6
X-RAY DIFFRACTION
r_nbd_other
0.176
0.2
43
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.115
0.2
12
X-RAY DIFFRACTION
r_mcbond_it
0.902
1.154
953
X-RAY DIFFRACTION
r_mcbond_other
0.894
1.154
953
X-RAY DIFFRACTION
r_mcangle_it
1.52
2.068
1186
X-RAY DIFFRACTION
r_mcangle_other
1.52
2.068
1187
X-RAY DIFFRACTION
r_scbond_it
1.425
1.216
999
X-RAY DIFFRACTION
r_scbond_other
1.409
1.214
997
X-RAY DIFFRACTION
r_scangle_it
2.34
2.174
1491
X-RAY DIFFRACTION
r_scangle_other
2.341
2.174
1491
X-RAY DIFFRACTION
r_lrange_it
3.621
11.871
2505
X-RAY DIFFRACTION
r_lrange_other
3.606
11.863
2502
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
1.8-1.847
0.258
83
0.233
1630
0.234
1797
0.949
0.959
95.3255
0.236
1.847-1.897
0.299
119
0.239
1494
0.244
1682
0.939
0.956
95.8977
0.244
1.897-1.952
0.282
69
0.23
1488
0.232
1643
0.944
0.958
94.7657
0.233
1.952-2.012
0.245
76
0.228
1479
0.229
1609
0.958
0.964
96.6439
0.239
2.012-2.078
0.275
79
0.238
1379
0.24
1522
0.919
0.95
95.795
0.247
2.078-2.15
0.201
78
0.21
1395
0.21
1531
0.971
0.969
96.2116
0.222
2.15-2.231
0.254
78
0.181
1285
0.185
1413
0.958
0.977
96.4614
0.194
2.231-2.322
0.271
89
0.196
1263
0.201
1399
0.954
0.972
96.6405
0.211
2.322-2.425
0.309
31
0.183
1273
0.186
1346
0.937
0.978
96.8796
0.198
2.425-2.543
0.224
37
0.188
1208
0.189
1283
0.967
0.977
97.0382
0.207
2.543-2.68
0.233
39
0.182
1123
0.184
1196
0.96
0.977
97.1572
0.201
2.68-2.841
0.259
65
0.175
1055
0.18
1145
0.962
0.979
97.8166
0.198
2.841-3.036
0.246
48
0.182
995
0.185
1066
0.964
0.976
97.8424
0.206
3.036-3.278
0.186
37
0.175
981
0.176
1037
0.975
0.979
98.1678
0.203
3.278-3.588
0.245
51
0.182
845
0.185
908
0.965
0.979
98.6784
0.22
3.588-4.007
0.239
42
0.178
794
0.181
844
0.97
0.977
99.0521
0.22
4.007-4.619
0.175
34
0.174
675
0.174
717
0.978
0.98
98.8842
0.221
4.619-5.637
0.191
52
0.177
582
0.178
644
0.978
0.981
98.4472
0.248
5.637-7.887
0.168
24
0.2
454
0.198
486
0.978
0.976
98.3539
0.296
7.887-38.457
0.703
4
0.187
268
0.19
275
0.678
0.966
98.9091
0.319
+
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