Resolution: 1.8→29.73 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.764 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. A SODIUM ION IS MODELLED BASED ON CRYSTALLIZATION CONDITION AND COORDINATION GEOMETRY. SODIUM ION IS COORDINATED IN AN OCTAHEDRAL GEOMETRY TO OD1 OF ASP52, OG OF SER 91 AND THREE WATER ...Details: 1. A SODIUM ION IS MODELLED BASED ON CRYSTALLIZATION CONDITION AND COORDINATION GEOMETRY. SODIUM ION IS COORDINATED IN AN OCTAHEDRAL GEOMETRY TO OD1 OF ASP52, OG OF SER 91 AND THREE WATER MOLECULES OF HOH2529, HOH2552 AND HOH2579. 2. THERE IS SOME UNKNOWN AND UNMODELLED DENSITY LOCATED NEAR THE PHENOL RING OF THE ZMA LIGAND, WHICH LIKELY REPRESENT AN ALTERNATIVE CONFORMATION OF THIS FLEXIBLE MOIETY. 3. DISORDERED LIPIDS INCLUDING OLA-2417, OLA-2419, OLC-2423, OLC-2427, OLC-2428 COULD REPRESENT FRAGMENTS OF PHOSPHOLIPID, CHOLESTEROL OR 1-OLEOYL-RAC-GLYCEROL.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.21313
2222
5 %
RANDOM
Rwork
0.17407
-
-
-
obs
0.17604
42032
94.5 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 27.398 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.05 Å2
0 Å2
0 Å2
2-
-
-0.13 Å2
0 Å2
3-
-
-
0.09 Å2
Refinement step
Cycle: LAST / Resolution: 1.8→29.73 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3012
0
481
177
3670
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.014
0.022
3653
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
2680
X-RAY DIFFRACTION
r_angle_refined_deg
1.584
2.065
4891
X-RAY DIFFRACTION
r_angle_other_deg
1.098
3
6560
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.711
5
412
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
38.746
23.548
124
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.558
15
524
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
21.081
15
16
X-RAY DIFFRACTION
r_chiral_restr
0.105
0.2
550
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
3778
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
717
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
1.481
3
2011
X-RAY DIFFRACTION
r_mcbond_other
0.45
3
812
X-RAY DIFFRACTION
r_mcangle_it
2.27
5
3253
X-RAY DIFFRACTION
r_scbond_it
4.026
8
1642
X-RAY DIFFRACTION
r_scangle_it
5.791
11
1638
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.8→1.847 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.329
147
-
Rwork
0.273
2809
-
obs
-
-
87.95 %
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
1.3047
1.6923
-0.5264
20.5751
-6.2518
3.295
0.0484
0.0377
0.0063
0.0644
0.1134
0.4664
-0.133
-0.1228
-0.1617
0.0567
0.0019
-0.002
0.1036
-0.004
0.0127
-10.9918
-3.9454
6.8744
2
19.5268
16.1895
-12.9421
23.952
-2.7492
15.0509
-0.9559
0.0523
-0.4134
-0.1951
0.601
0.4029
1.1611
0.3751
0.3549
0.2441
-0.0184
-0.0766
0.0949
0.0845
0.5072
-10.3295
-29.8316
14.7622
3
1.7642
-1.0193
0.5252
3.6582
-0.823
1.3426
-0.0068
-0.0812
-0.0569
-0.0716
0.1231
0.1718
0.0548
-0.1406
-0.1163
0.0468
-0.0017
0.0043
0.0853
0.0083
0.0164
-10.1582
-5.0186
17.3034
4
3.8666
-6.6088
-0.216
14.9615
0.1919
0.8786
-0.1526
-0.1627
0.1288
0.3771
0.1149
-0.3673
0.0801
0.011
0.0377
0.0518
-0.0024
-0.0169
0.0923
0.0014
0.015
-1.9496
-10.7814
24.2306
5
14.8029
-10.1338
-9.5771
21.7072
-1.2422
10.3164
-0.6072
-0.7783
-0.491
-0.0576
0.1444
-0.0296
0.6201
0.6694
0.4628
0.3188
-0.0056
-0.0231
0.2568
0.0979
0.1925
0.9067
-33.0684
28.5603
6
1.2035
-1.2283
-0.1009
21.4041
-1.9229
0.5095
-0.1843
-0.0734
-0.2107
0.6621
0.2288
0.2235
0.1749
0.0245
-0.0444
0.1981
0.0268
-0.0007
0.1135
0.0262
0.0599
-7.8641
-13.865
29.7137
7
6.1179
-3.831
3.2495
3.2583
-1.1023
3.7961
-0.3817
0.1872
0.9081
0.1153
-0.182
-0.1317
-0.8552
-0.0753
0.5638
0.2985
0.0409
0.0697
0.1563
0.0315
0.5053
-6.9818
17.0669
27.1623
8
4.6764
-3.7345
1.1163
5.4095
-0.4474
2.3606
0.0343
0.0099
0.0618
-0.0091
-0.0933
0.1967
-0.1207
0.0175
0.059
0.0515
-0.0136
0.0054
0.0812
-0.0055
0.0453
0.4102
7.2803
25.433
9
2.0881
-5.4485
-1.6028
21.8699
6.2025
2.4787
-0.0124
-0.0747
0.0098
0.2971
0.141
-0.8825
0.1498
0.1408
-0.1286
0.1107
0.0272
-0.0205
0.1176
-0.0098
0.1639
13.0473
-20.872
21.8023
10
0.72
0.5337
0.2162
6.393
0.6548
0.8604
-0.0305
0.0484
-0.1623
-0.2663
0.1347
-0.3255
0.1498
0.121
-0.1042
0.0731
0.0299
0.0115
0.0946
0.0051
0.0742
7.6709
-13.3465
15.0381
11
7.0264
-4.2003
10.9282
8.2942
-1.6781
21.0838
-0.9217
-0.067
0.491
0.4595
0.5554
-0.6952
-1.2802
0.4163
0.3662
0.2705
0.0384
0.0381
0.1962
0.052
0.2057
11.1396
16.2083
17.3125
12
0.9128
2.0947
0.4242
13.733
1.0745
1.1449
-0.0166
0.0785
0.0003
-0.4142
-0.0077
-0.0309
0.0272
0.0363
0.0242
0.0569
0.0221
0.0004
0.107
0.0165
0.0179
-0.4175
-5.0165
8.2951
13
22.3732
-1.277
6.319
11.2448
-0.0488
13.3027
0.2163
1.142
-0.7201
-0.983
-0.072
0.5361
0.6687
-0.3328
-0.1443
0.3223
-0.0784
-0.0227
0.1721
-0.0436
0.1214
-10.487
-25.2207
2.7877
14
14.3514
-19.9233
-1.9101
38.5212
1.4838
1.7664
0.2725
0.146
0.435
-0.989
-0.5419
-1.6647
0.1872
0.164
0.2694
0.2887
0.0665
0.1044
0.2415
0.0185
0.6371
25.7603
-49.3985
16.1997
15
17.2785
-13.6158
-2.7492
24.2101
-4.7961
6.769
-0.4648
-1.1799
1.7658
1.0732
0.6136
-1.4639
-0.5001
0.2215
-0.1488
0.3548
0.0591
-0.2118
0.3251
-0.2213
0.8615
24.5547
-53.4454
25.5883
16
27.1612
-17.4107
8.3216
23.1118
-9.6204
13.8851
-0.4466
-1.374
0.143
0.6583
1.3132
1.4145
-0.2563
-1.0919
-0.8665
0.2375
0.0551
0.0497
0.2831
0.0772
0.5244
15.0374
-57.9403
23.7417
17
24.1901
-14.5038
6.7759
18.4892
-2.9948
14.5502
-0.3005
-0.4649
0.2023
-0.7867
-0.0522
-0.1043
0.7266
0.2125
0.3527
0.2893
0.0763
0.0226
0.1325
-0.0142
0.4557
26.536
-65.9659
18.9084
18
11.3951
-14.2936
8.2104
32.8026
1.7017
15.6122
1.4333
0.4974
-0.6457
-1.9857
-0.4732
0.2107
0.832
0.4045
-0.9601
0.4562
0.059
-0.1223
0.195
0.0722
0.61
15.9315
-55.601
12.964
19
44.0898
7.508
-6.952
40.5722
-11.0641
16.1501
-0.2723
-0.4155
-1.6832
-1.748
0.1661
0.4682
0.5312
0.0561
0.1062
0.3548
0.0913
-0.15
0.1207
0.0082
0.5447
11.8641
-47.555
13.4572
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
-1 - 34
2
X-RAY DIFFRACTION
2
A
35 - 38
3
X-RAY DIFFRACTION
3
A
39 - 73
4
X-RAY DIFFRACTION
4
A
74 - 108
5
X-RAY DIFFRACTION
5
A
109 - 117
6
X-RAY DIFFRACTION
6
A
118 - 137
7
X-RAY DIFFRACTION
7
A
138 - 161
8
X-RAY DIFFRACTION
8
A
162 - 186
9
X-RAY DIFFRACTION
9
A
187 - 208
10
X-RAY DIFFRACTION
10
A
219 - 259
11
X-RAY DIFFRACTION
11
A
260 - 265
12
X-RAY DIFFRACTION
12
A
266 - 292
13
X-RAY DIFFRACTION
13
A
293 - 307
14
X-RAY DIFFRACTION
14
A
1001 - 1021
15
X-RAY DIFFRACTION
15
A
1022 - 1042
16
X-RAY DIFFRACTION
16
A
1058 - 1081
17
X-RAY DIFFRACTION
17
A
1082 - 1093
18
X-RAY DIFFRACTION
18
A
1094 - 1101
19
X-RAY DIFFRACTION
19
A
1102 - 1106
+
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