Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.25 Å3/Da / Density % sol: 45.24 %
Crystal grow
Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Protein buffer: 10 mg/mL Protein, 0.1 M NaCl, 0.05 M Tris-HCl pH 8.0, 0.001 M TCEP, 0.001 M CaCl2, 0.001 M MgCl2, 0.001 M MnCl2. Precipitant: 2 M Na/K PO4, pH 7.0. Cryoprotectant: 20% ...Details: Protein buffer: 10 mg/mL Protein, 0.1 M NaCl, 0.05 M Tris-HCl pH 8.0, 0.001 M TCEP, 0.001 M CaCl2, 0.001 M MgCl2, 0.001 M MnCl2. Precipitant: 2 M Na/K PO4, pH 7.0. Cryoprotectant: 20% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K
-
Data collection
Diffraction
Mean temperature: 100 K
Diffraction source
Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
Resolution: 1.81→24.16 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.764 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS, ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.18203
1202
4.9 %
RANDOM
Rwork
0.14759
-
-
-
obs
0.14931
23192
99.93 %
-
all
-
24394
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 13.151 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.29 Å2
0 Å2
0 Å2
2-
-
-0.57 Å2
0 Å2
3-
-
-
-0.72 Å2
Refinement step
Cycle: LAST / Resolution: 1.81→24.16 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1931
0
29
187
2147
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.019
0.021
2098
X-RAY DIFFRACTION
r_angle_refined_deg
1.618
1.966
2838
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.317
5
249
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
28.426
23.333
108
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.608
15
378
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
21.882
15
22
X-RAY DIFFRACTION
r_chiral_restr
0.123
0.2
304
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.02
1597
X-RAY DIFFRACTION
r_nbd_refined
0.212
0.2
941
X-RAY DIFFRACTION
r_nbtor_refined
0.309
0.2
1437
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.131
0.2
189
X-RAY DIFFRACTION
r_metal_ion_refined
0.184
0.2
2
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.162
0.2
50
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.135
0.2
9
X-RAY DIFFRACTION
r_mcbond_it
0.968
1.5
1271
X-RAY DIFFRACTION
r_mcangle_it
1.318
2
2005
X-RAY DIFFRACTION
r_scbond_it
2.517
3
942
X-RAY DIFFRACTION
r_scangle_it
3.597
4.5
833
LS refinement shell
Resolution: 1.81→1.86 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.243
81
-
Rwork
0.145
1643
-
obs
-
-
99.14 %
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
21.4347
6.4268
-4.1197
20.7715
15.0022
15.2593
-0.2256
-0.6937
-0.3339
-0.3155
0.0494
-0.2499
-0.3133
-0.0099
0.1762
0.0421
-0.0333
-0.0029
0.0355
0.0371
0.0237
35.161
15.5511
34.9395
2
23.65
-12.5358
25.3619
18.2387
-10.917
35.0751
0.1655
-0.3504
0.7093
-0.3616
-0.5562
-0.3034
0.6875
-0.2594
0.3906
0.0286
0.0227
0.0315
0.0927
0.0074
0.0147
26.4691
22.3825
35.0795
3
2.2811
-0.2546
0.5835
4.3234
2.1324
7.1037
-0.0289
-0.0175
-0.0391
0.0792
-0.0102
0.2773
-0.0905
-0.4988
0.0391
0.0554
0.0095
0.0394
0.0789
0.0384
0.0665
17.3297
23.4821
22.8648
4
7.5792
-7.9425
-8.1814
21.9522
16.7479
13.7342
-0.1965
0.2038
0.1426
0.3933
-0.1189
0.276
0.6324
-0.409
0.3154
0.0728
0.0005
-0.0056
0.048
0.0007
0.0664
22.6756
14.2106
16.7294
5
8.8795
0.4727
-5.1549
4.6463
-0.8951
7.0609
-0.1286
-0.1751
-0.1785
0.0025
-0.0802
-0.3508
0.3719
0.3416
0.2088
0.059
0.0354
0.013
0.0556
0.0016
0.0841
36.8471
11.1271
8.6843
6
3.6702
2.2964
1.5051
2.0336
-0.1402
2.5785
-0.0015
-0.0478
-0.0631
0.2074
0.0038
-0.0768
0.0736
0.0499
-0.0023
0.1004
0.0114
0.0068
0.0571
0.0145
0.0636
30.2543
16.0152
21.1849
7
0.5518
-0.3177
0.1939
1.1528
-0.5095
1.0639
0.0184
0.0343
-0.0229
-0.024
-0.027
0.03
0.0853
0.0493
0.0086
0.0572
0.0059
-0.0012
0.0831
0.006
0.0727
30.8968
24.0019
7.8914
8
1.0372
0.137
-0.651
1.0538
-1.7026
4.0455
0.0053
-0.0058
-0.0242
0.0498
0.0082
0.0879
-0.0501
0.0084
-0.0134
0.0764
0.0069
0.01
0.0625
0.0015
0.0797
24.5404
34.4307
12.3607
9
0.3751
0.3293
0.09
3.0728
-1.1473
1.5986
0.0235
0.0703
-0.0313
-0.0729
0.0255
-0.0658
0.217
-0.0188
-0.0489
0.059
-0.0102
-0.0057
0.0732
-0.0111
0.0894
25.5846
14.7651
4.7549
10
3.6443
-4.481
-1.4121
6.1715
2.511
2.5392
0.0055
0.2212
-0.0863
-0.0706
-0.0477
0.2366
0.1138
-0.1792
0.0422
0.0634
-0.0209
-0.0036
0.0711
-0.0013
0.0826
22.1566
20.0749
1.4492
11
3.9608
-0.3859
0.5665
1.5258
0.6411
0.5951
0.2195
0.0493
-0.4482
-0.12
-0.004
0.072
0.156
-0.1565
-0.2154
0.0699
0.0293
-0.0354
0.0595
-0.0001
0.12
16.0498
26.8889
-0.4448
12
10.5955
-2.9935
1.2342
2.5467
0.1486
4.1693
0.3128
0.5609
-0.4888
-0.1986
-0.2312
0.0749
0.1254
-0.0403
-0.0816
0.079
0.0154
-0.0046
0.061
-0.0242
0.0647
30.2866
23.8693
-3.7507
13
1.5907
-0.6496
-2.0482
1.8901
0.0565
3.913
0.041
-0.0992
-0.0331
0.0954
-0.0452
-0.0753
-0.0721
0.1339
0.0042
0.0537
-0.0047
-0.0086
0.0886
0
0.0789
34.9043
23.53
17.2105
14
2.7174
-1.615
0.3634
1.0421
-0.5754
1.6183
0.0696
0.2111
-0.0326
-0.2198
-0.0724
0.0376
0.1135
-0.0727
0.0028
0.0625
-0.0103
-0.0349
0.0795
0.0121
0.1055
23.9021
30.4351
-1.8873
15
2.3207
0.0931
1.2932
2.3462
0.1527
2.5173
-0.0196
-0.0478
0.0291
-0.0481
0.02
0.1683
0.0055
-0.2099
-0.0004
0.0699
0.0064
0.0252
0.079
0.0071
0.0798
15.761
32.8451
12.5775
16
5.3184
0.7669
3.759
1.2965
0.2262
5.2984
0.0755
-0.0387
0.1935
0.0278
-0.0281
0.0622
-0.0218
0.0852
-0.0474
0.0715
0.0023
0.0252
0.0569
0.0079
0.0692
30.3871
43.9451
5.5941
17
2.3243
0.0089
-1.6565
7.0879
4.2213
9.8229
0.0717
0.0532
0.1204
0.304
0.0574
-0.2253
-0.1604
0.2616
-0.1291
0.0868
-0.0054
-0.0046
0.0557
0.0078
0.0576
33.9356
44.7102
17.0519
18
4.1014
-0.2034
-3.4752
0.0595
-0.1178
4.649
-0.0148
-0.1256
-0.1085
0.0391
0.0109
-0.1866
0.0893
0.1641
0.0039
0.0759
0.0111
0.0014
0.0647
-0.0075
0.0847
36.4771
33.8607
8.0606
19
0.5129
-1.3895
0.4515
9.3834
4.7721
6.7927
0.2268
0.1006
0.0411
-0.4069
-0.1757
-0.0293
-0.0953
0.0839
-0.0511
0.0986
0.0031
0.0474
0.0806
-0.0027
0.0411
35.1716
36.7223
-5.529
20
1.5168
-1.0183
1.7468
2.123
-0.107
4.4062
0.0702
0.0747
-0.0562
-0.1635
0.0516
-0.0263
-0.0483
0.2668
-0.1218
0.0686
0.0027
0.0495
0.0659
-0.0127
0.0651
40.4553
24.4504
-2.1326
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Label asym-ID
Auth seq-ID
Label seq-ID
1
X-RAY DIFFRACTION
1
A
A
-5 - -1
14 - 18
2
X-RAY DIFFRACTION
2
A
A
0 - 5
19 - 24
3
X-RAY DIFFRACTION
3
A
A
6 - 16
25 - 35
4
X-RAY DIFFRACTION
4
A
A
17 - 21
36 - 40
5
X-RAY DIFFRACTION
5
A
A
22 - 32
41 - 51
6
X-RAY DIFFRACTION
6
A
A
33 - 45
52 - 64
7
X-RAY DIFFRACTION
7
A
A
46 - 61
65 - 80
8
X-RAY DIFFRACTION
8
A
A
62 - 83
81 - 102
9
X-RAY DIFFRACTION
9
A
A
84 - 99
103 - 118
10
X-RAY DIFFRACTION
10
A
A
100 - 114
119 - 133
11
X-RAY DIFFRACTION
11
A
A
115 - 125
134 - 144
12
X-RAY DIFFRACTION
12
A
A
126 - 133
145 - 152
13
X-RAY DIFFRACTION
13
A
A
134 - 150
153 - 169
14
X-RAY DIFFRACTION
14
A
A
151 - 161
170 - 180
15
X-RAY DIFFRACTION
15
A
A
162 - 171
181 - 190
16
X-RAY DIFFRACTION
16
A
A
172 - 183
191 - 202
17
X-RAY DIFFRACTION
17
A
A
184 - 192
203 - 211
18
X-RAY DIFFRACTION
18
A
A
193 - 205
212 - 224
19
X-RAY DIFFRACTION
19
A
A
206 - 214
225 - 233
20
X-RAY DIFFRACTION
20
A
A
215 - 227
234 - 246
+
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