F1F0 ATP synthase subunit C / F1FO ATP Synthase / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / Up-down Bundle / Mainly Alpha Similarity search - Domain/homology
Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.211 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22771
2828
5.1 %
RANDOM
Rwork
0.20178
-
-
-
obs
0.20309
53035
98.11 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 26.787 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.97 Å2
0 Å2
0 Å2
2-
-
0.97 Å2
0 Å2
3-
-
-
-1.94 Å2
Refinement step
Cycle: LAST / Resolution: 1.9→30 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5301
0
392
150
5843
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.01
0.02
6034
X-RAY DIFFRACTION
r_angle_refined_deg
1.181
2.066
8273
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
3.861
5
837
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
38.558
23.077
130
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.315
15
895
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
8.82
15
10
X-RAY DIFFRACTION
r_chiral_restr
0.069
0.2
1119
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.021
4102
LS refinement shell
Resolution: 1.9→1.949 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.269
164
-
Rwork
0.247
3219
-
obs
-
3219
88.49 %
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
0.8219
0.0584
-1.4088
0.6048
-0.8813
12.1049
0.0048
-0.1528
0.0733
0.0891
0.0385
-0.0344
-0.1763
0.2207
-0.0433
0.0144
0.0057
-0.0123
0.0329
-0.0124
0.0566
48.1731
8.4428
31.9563
2
0.5515
0.226
-1.2695
0.7242
-1.503
15.4055
-0.0108
-0.165
0.0209
0.1228
-0.0486
-0.0668
-0.1658
0.6622
0.0594
0.0615
-0.0174
-0.0092
0.0758
-0.0151
0.12
50.6378
16.2729
28.028
3
0.824
0.0914
-1.2961
0.7042
-1.9114
15.0796
0.0893
-0.1499
0.078
0.0963
0.0822
0.0303
-0.168
0.0335
-0.1715
0.0259
-0.0026
0.0018
0.0412
-0.0125
0.0652
41.2095
12.8698
31.9539
4
0.6854
-0.0157
-0.4424
0.7935
-1.8507
13.6008
0.0025
-0.1701
0.1212
0.1561
0.0011
0.0164
-0.7232
0.1819
-0.0036
0.0791
-0.0103
-0.0008
0.0439
-0.0294
0.1169
38.5893
20.7572
28.4743
5
0.675
0.0489
0.1942
0.6393
-1.6584
15.0917
0.0553
-0.135
0.0322
0.1151
0.048
0.0701
-0.1548
0.0099
-0.1033
0.0267
0.0028
0.0052
0.0371
-0.0086
0.0744
33.0073
12.3523
32.0651
6
0.7009
-0.003
0.7812
0.5189
-1.801
15.1225
-0.018
-0.1519
0.0662
0.1702
0.0408
0.041
-0.6939
-0.0897
-0.0228
0.0745
0.028
0.0007
0.0523
-0.0237
0.1189
26.3972
17.1864
28.4715
7
0.7744
-0.0545
0.7427
0.7095
-1.4378
14.4843
0.0932
-0.1307
0.0154
0.1219
0.1097
0.0658
-0.0677
-0.0114
-0.2029
0.0351
0.0056
0.0103
0.0454
-0.004
0.0751
26.6863
7.1151
31.9921
8
0.58
0.0015
1.3064
0.4191
-0.8644
13.3215
-0.0065
-0.1807
0.035
0.1099
-0.0055
0.0778
-0.396
-0.5325
0.012
0.0433
0.0219
0.0128
0.09
-0.0123
0.1184
18.429
7.1931
28.8376
9
0.796
-0.1507
1.6345
0.6979
-0.2709
15.5128
0.0447
-0.1643
-0.0239
0.1279
0.1257
0.0931
-0.0473
-0.128
-0.1705
0.0317
0.0076
0.018
0.0529
0.0031
0.0704
24.5122
-0.8284
32.1383
10
0.4103
-0.0452
2.0871
0.6511
0.2567
14.5488
0.0073
-0.1936
-0.0169
0.1373
-0.0558
0.0805
0.0151
-0.8086
0.0485
0.0342
-0.0281
0.0169
0.1161
0.007
0.1253
17.7678
-5.6123
28.5088
11
0.9255
0.2872
0.6838
0.7389
1.1061
8.9304
0.159
-0.2307
-0.0671
0.1861
-0.0397
0.0247
0.2891
-0.1016
-0.1193
0.0579
-0.0346
0.0083
0.0605
0.0096
0.0653
-8.4864
27.604
31.9374
12
0.2668
-0.0732
0.1043
0.6502
1.5445
13.4193
-0.0097
-0.1614
-0.0233
0.1961
-0.1171
0.0215
0.4837
-0.5614
0.1268
0.1161
-0.0749
0.009
0.1574
0.0205
0.1191
-9.4689
19.3737
28.7293
13
0.7099
0.2847
1.001
0.7273
1.8687
13.9366
0.1572
-0.212
-0.0529
0.1855
-0.0162
-0.0582
0.281
-0.0928
-0.1411
0.0652
-0.0337
-0.0162
0.0725
0.0224
0.0825
-0.9237
24.5781
31.8681
14
0.7338
-0.0335
0.0652
0.5067
2.6501
15.5946
-0.0143
-0.2282
-0.1134
0.2129
-0.0516
-0.0275
0.8879
-0.1391
0.0659
0.1581
-0.0411
-0.0175
0.1013
0.062
0.1452
3.0377
17.2453
28.8045
15
0.6132
0.0791
-0.4728
0.8259
1.6034
14.1251
0.1898
-0.2081
-0.0682
0.194
0.0146
-0.0538
0.149
0.1944
-0.2044
0.0933
-0.0547
-0.0265
0.0761
0.0373
0.0846
7.0446
26.5466
32.2231
16
1.2711
0.1899
-1.0205
1.127
2.5229
19.1346
0.0454
-0.2958
-0.1093
0.2723
-0.0515
-0.0757
0.7628
0.2981
0.0062
0.0783
-0.0012
-0.0329
0.089
0.043
0.135
14.5586
23.1977
28.1522
17
0.8659
0.0697
-1.3076
0.6575
1.2604
11.0828
0.1293
-0.2295
-0.0013
0.1843
-0.0199
-0.0579
0.2767
0.133
-0.1094
0.0673
-0.0383
-0.0158
0.0766
0.0263
0.0825
12.4057
32.8565
32.6788
18
1.3026
-0.0254
-1.3204
0.6589
0.8082
14.9666
0.0574
-0.2805
-0.0886
0.1867
-0.0133
-0.0573
0.5484
0.5544
-0.0442
0.0706
-0.0141
-0.0405
0.0796
0.047
0.1275
20.4216
34.3446
28.8159
19
1.0167
-0.0225
-1.7896
0.7519
0.504
10.6683
0.1134
-0.2252
0.0041
0.1713
-0.0482
-0.0693
0.0453
0.1517
-0.0652
0.0559
-0.0423
-0.0216
0.0614
0.0145
0.0727
12.9696
41.1907
32.343
20
1.0485
0.1764
-2.4694
0.7492
-0.5725
15.0248
0.0179
-0.2761
-0.0059
0.1932
-0.1301
-0.0542
0.0154
0.611
0.1122
0.0718
-0.0495
-0.0254
0.1078
0.0108
0.1156
18.5135
47.1106
28.7013
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
1 - 41
2
X-RAY DIFFRACTION
2
A
42 - 74
3
X-RAY DIFFRACTION
3
B
1 - 41
4
X-RAY DIFFRACTION
4
B
42 - 75
5
X-RAY DIFFRACTION
5
C
1 - 41
6
X-RAY DIFFRACTION
6
C
42 - 75
7
X-RAY DIFFRACTION
7
D
1 - 41
8
X-RAY DIFFRACTION
8
D
42 - 75
9
X-RAY DIFFRACTION
9
E
1 - 41
10
X-RAY DIFFRACTION
10
E
42 - 75
11
X-RAY DIFFRACTION
11
K
1 - 41
12
X-RAY DIFFRACTION
12
K
42 - 75
13
X-RAY DIFFRACTION
13
L
1 - 41
14
X-RAY DIFFRACTION
14
L
42 - 75
15
X-RAY DIFFRACTION
15
M
1 - 41
16
X-RAY DIFFRACTION
16
M
42 - 75
17
X-RAY DIFFRACTION
17
N
1 - 41
18
X-RAY DIFFRACTION
18
N
42 - 75
19
X-RAY DIFFRACTION
19
O
1 - 41
20
X-RAY DIFFRACTION
20
O
42 - 75
+
About Yorodumi
-
News
-
Feb 9, 2022. New format data for meta-information of EMDB entries
New format data for meta-information of EMDB entries
Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi