Cytochromeb-c1complexsubunit1, mitochondrial / Complex III subunit 1 / Core protein I / Ubiquinol-cytochrome-c reductase complex core protein 1
Mass: 52796.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P31800
#2: Protein
Cytochromeb-c1complexsubunit2, mitochondrial / Complex III subunit 2 / Core protein II / Ubiquinol-cytochrome-c reductase complex core protein 2
Mass: 48203.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P23004
#5: Protein
Cytochromeb-c1complexsubunitRieske, mitochondrial / Complex III subunit 5 / Cytochrome b-c1 complex subunit 5 / Rieske iron-sulfur protein / RISP / ...Complex III subunit 5 / Cytochrome b-c1 complex subunit 5 / Rieske iron-sulfur protein / RISP / Rieske protein UQCRFS1 / Ubiquinol-cytochrome c reductase iron-sulfur subunit
Mass: 29586.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P13272, quinol-cytochrome-c reductase
#6: Protein
Cytochromeb-c1complexsubunit7 / Complex III subunit 7 / Complex III subunit VII / QP-C / Ubiquinol-cytochrome c reductase complex ...Complex III subunit 7 / Complex III subunit VII / QP-C / Ubiquinol-cytochrome c reductase complex 14 kDa protein
Mass: 13501.401 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00129
#7: Protein
Cytochromeb-c1complexsubunit8 / Complex III subunit 8 / Complex III subunit VIII / Ubiquinol-cytochrome c reductase complex 9.5 kDa ...Complex III subunit 8 / Complex III subunit VIII / Ubiquinol-cytochrome c reductase complex 9.5 kDa protein / Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C
Mass: 9737.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P13271
#8: Protein
Cytochromeb-c1complexsubunit6, mitochondrial / Complex III subunit 6 / Complex III subunit VIII / Cytochrome c1 non-heme 11 kDa protein / ...Complex III subunit 6 / Complex III subunit VIII / Cytochrome c1 non-heme 11 kDa protein / Mitochondrial hinge protein / Ubiquinol-cytochrome c reductase complex 11 kDa protein
Mass: 12346.647 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: A0A452DIC1
#9: Protein
Cytochromeb-c1complexsubunit9 / Complex III subunit 9 / Complex III subunit X / Cytochrome c1 non-heme 7 kDa protein / Ubiquinol- ...Complex III subunit 9 / Complex III subunit X / Cytochrome c1 non-heme 7 kDa protein / Ubiquinol-cytochrome c reductase complex 7.2 kDa protein
Mass: 7469.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00130
#10: Protein
Cytochromeb-c1complexsubunit10 / Complex III subunit 10 / Complex III subunit XI / Ubiquinol-cytochrome c reductase complex 6.4 kDa protein
Mass: 6527.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P07552
-
Protein , 2 types, 2 molecules CD
#3: Protein
Cytochromeb / Complex III subunit 3 / Complex III subunit III / Cytochrome b-c1 complex subunit 3 / Ubiquinol- ...Complex III subunit 3 / Complex III subunit III / Cytochrome b-c1 complex subunit 3 / Ubiquinol-cytochrome-c reductase complex cytochrome b subunit
Mass: 42620.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00157
#4: Protein
Cytochromec1, hemeprotein, mitochondrial / Complex III subunit 4 / Complex III subunit IV / Cytochrome b-c1 complex subunit 4 / Ubiquinol- ...Complex III subunit 4 / Complex III subunit IV / Cytochrome b-c1 complex subunit 4 / Ubiquinol-cytochrome-c reductase complex cytochrome c1 subunit / Cytochrome c-1
Mass: 35343.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00125
Resolution: 3.54→3.62 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3699 / CC1/2: 0.54 / Rpim(I) all: 0.51 / % possible all: 96.5
-
Processing
Software
Name
Version
Classification
REFMAC
5.8.0425
refinement
MOSFLM
datareduction
Aimless
datascaling
MOLREP
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.522→30 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.873 / SU B: 57.112 / SU ML: 0.373 / Cross valid method: FREE R-VALUE / ESU R Free: 0.487 / Details: Hydrogens have not been used
Rfactor
Num. reflection
% reflection
Rfree
0.2407
2830
5.085 %
Rwork
0.1877
52827
-
all
0.19
-
-
obs
-
55657
99.106 %
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: 124.215 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.316 Å2
-0.158 Å2
-0 Å2
2-
-
-0.316 Å2
0 Å2
3-
-
-
1.026 Å2
Refinement step
Cycle: LAST / Resolution: 3.522→30 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
15866
0
813
10
16689
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.007
0.012
17108
X-RAY DIFFRACTION
r_angle_refined_deg
2.081
1.841
23149
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.5
5
2019
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
16.924
5.137
146
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.96
10
2646
X-RAY DIFFRACTION
r_dihedral_angle_6_deg
14.327
10
723
X-RAY DIFFRACTION
r_chiral_restr
0.133
0.2
2503
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
12746
X-RAY DIFFRACTION
r_nbd_refined
0.237
0.2
7870
X-RAY DIFFRACTION
r_nbtor_refined
0.318
0.2
11457
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.154
0.2
431
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.235
0.2
196
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.383
0.2
13
X-RAY DIFFRACTION
r_mcbond_it
7.758
8.402
8103
X-RAY DIFFRACTION
r_mcangle_it
11.98
15.095
10107
X-RAY DIFFRACTION
r_scbond_it
10.54
8.86
9005
X-RAY DIFFRACTION
r_scangle_it
15.641
16.126
13038
X-RAY DIFFRACTION
r_lrange_it
19.372
105.296
70944
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
3.522-3.614
0.348
200
0.304
3699
X-RAY DIFFRACTION
95.94
3.614-3.712
0.333
191
0.269
3753
X-RAY DIFFRACTION
99.7723
3.712-3.819
0.315
186
0.245
3663
X-RAY DIFFRACTION
99.8444
3.819-3.936
0.276
213
0.219
3506
X-RAY DIFFRACTION
99.7318
3.936-4.064
0.279
157
0.21
3484
X-RAY DIFFRACTION
99.7534
4.064-4.206
0.22
177
0.192
3346
X-RAY DIFFRACTION
99.6324
4.206-4.363
0.224
187
0.164
3194
X-RAY DIFFRACTION
99.529
4.363-4.54
0.2
177
0.151
3082
X-RAY DIFFRACTION
99.4811
4.54-4.74
0.183
167
0.139
2973
X-RAY DIFFRACTION
99.6193
4.74-4.969
0.202
165
0.132
2860
X-RAY DIFFRACTION
99.5721
4.969-5.235
0.214
139
0.144
2740
X-RAY DIFFRACTION
99.3444
5.235-5.549
0.245
126
0.165
2593
X-RAY DIFFRACTION
99.5242
5.549-5.926
0.239
121
0.17
2444
X-RAY DIFFRACTION
99.3416
5.926-6.394
0.239
119
0.194
2310
X-RAY DIFFRACTION
99.1833
6.394-6.992
0.22
118
0.182
2108
X-RAY DIFFRACTION
99.2864
6.992-7.798
0.213
100
0.155
1920
X-RAY DIFFRACTION
98.9226
7.798-8.968
0.174
92
0.137
1720
X-RAY DIFFRACTION
98.5318
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
1.3385
-0.0545
-0.0044
1.9794
-0.2582
1.9757
-0.0092
0.2863
0.4624
-0.1479
-0.0103
-0.1803
-0.1732
0.118
0.0194
0.043
-0.0565
-0.0346
0.2114
0.2448
0.3222
-92.3606
-31.3848
7.3632
2
1.5475
-0.5076
-0.4997
1.4331
-0.084
0.9736
0.0073
0.3644
0.2777
-0.1829
-0.0196
0.2896
-0.2129
-0.2011
0.0123
0.1158
-0.0343
-0.1441
0.261
0.2122
0.3119
-122.704
-40.5318
7.2422
3
1.4003
-0.7085
-0.225
1.3343
0.1636
0.9953
-0.1299
-0.1816
0.0117
0.3181
0.085
-0.3128
0.0791
0.3508
0.0449
0.1088
0.0695
-0.0858
0.2606
0.0406
0.2068
-56.7333
-71.013
42.5753
4
1.8556
-0.2247
0.6882
0.468
-0.0952
0.6174
-0.2418
-0.0574
0.1752
0.1712
0.1548
-0.5002
0.0547
0.4194
0.087
0.2142
0.2077
-0.1147
0.7766
-0.0502
0.6726
-28.021
-73.7337
30.5396
5
1.395
-1.5767
-0.5136
2.9072
0.9172
0.8775
-0.1225
0.3599
-0.3694
-0.183
0.1366
0.0242
0.3454
0.3367
-0.0142
0.3814
0.007
0.108
0.7444
-0.0315
0.5736
-43.381
-84.3014
2.8424
6
3.2724
1.6611
-1.2489
3.1743
-2.1322
3.0873
0.0564
-0.4482
0.4955
0.4766
0.0716
-0.0279
0.015
0.2471
-0.128
0.2249
0.0974
-0.0705
0.1492
-0.1041
0.1742
-80.8198
-46.1933
52.1757
7
2.8897
-1.8254
1.923
1.7393
-1.3988
1.6179
-0.289
0.0081
0.6288
0.2738
-0.0763
-0.5854
-0.0799
0.3033
0.3652
0.2671
-0.0046
-0.1484
0.4109
-0.0255
0.3388
-56.736
-49.2142
42.7513
8
1.6437
0.4912
-0.297
0.248
-0.6678
4.6316
0.0951
-0.0113
0.1347
0.1661
-0.1476
-0.0801
-0.1449
0.794
0.0525
0.5908
0.0498
-0.2231
0.8886
-0.0892
0.9833
-11.229
-62.8592
51.4948
9
2.2135
2.0145
3.0584
7.1106
5.0805
5.3957
-0.2984
-0.2808
0.1269
-0.3229
0.534
-0.2863
-0.6043
0.064
-0.2356
0.4644
-0.1259
0.0931
0.5385
0.0103
0.5227
-112.4797
-35.6279
14.5321
10
3.2324
-1.1728
-0.1402
1.1778
0.2879
0.5831
0.22
0.9095
0.4475
-0.3124
-0.2262
-0.4582
-0.1004
0.4462
0.0062
0.1429
-0.0095
0.1298
0.6882
0.1926
0.4715
-43.5908
-57.2692
8.1652
11
5.1001
4.181
-0.2682
3.6737
0.1303
1.2038
-0.5988
0.4914
-0.5028
-0.301
0.2175
-0.248
-0.4154
0.1513
0.3813
1.1578
-0.0024
0.1224
1.0436
-0.0653
0.7426
-58.8381
-63.6484
-2.9127
Refinement TLS group
Selection: ALL
+
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