SIDE SCATTERING I-BEAM BENT SINGLE CRYSTAL, SI(111)
SINGLEWAVELENGTH
M
x-ray
1
2
KOHZUMONOCHROMATOR, DOUBLECRYSTAL, SI(111)
MAD
M
x-ray
2
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.97607
1
2
0.97903
1
3
0.97923
1
4
0.96104
1
Reflection
Resolution: 2.39→50 Å / Num. obs: 48090 / % possible obs: 99.8 % / Redundancy: 7 % / Rsym value: 0.128 / Net I/σ(I): 16.4
Reflection shell
Resolution: 2.39→2.49 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.466 / % possible all: 99
-
Processing
Software
Name
Version
Classification
Blu-Ice
datacollection
SOLVE
phasing
REFMAC
5.2.0019
refinement
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: MAD / Resolution: 2.39→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.903 / SU B: 15.596 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.261
2430
5.1 %
RANDOM
Rwork
0.193
-
-
-
obs
0.196
45669
99.3 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 43.222 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.06 Å2
0 Å2
0 Å2
2-
-
1.21 Å2
0 Å2
3-
-
-
-0.16 Å2
Refinement step
Cycle: LAST / Resolution: 2.39→50 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
7675
0
102
168
7945
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.028
0.021
7909
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
2.518
1.958
10769
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
8.325
5
981
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.67
23.085
389
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
21.101
15
1247
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
22.685
15
90
X-RAY DIFFRACTION
r_chiral_restr
0.21
0.2
1247
X-RAY DIFFRACTION
r_gen_planes_refined
0.01
0.02
6026
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.252
0.2
3180
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.31
0.2
5001
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.168
0.2
349
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
0.204
0.2
10
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.254
0.2
60
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.229
0.2
14
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
1.116
1.5
4910
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
1.948
2
7900
X-RAY DIFFRACTION
r_scbond_it
3.452
3
3017
X-RAY DIFFRACTION
r_scangle_it
5.254
4.5
2869
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.39→2.45 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.293
170
-
Rwork
0.22
2979
-
obs
-
-
90.99 %
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
3.4567
0.4632
-0.2484
1.5946
-0.4551
3.0637
0.076
0.2071
0.1918
-0.1396
-0.0535
0.1042
-0.0542
0.054
-0.0225
-0.0592
0.0208
-0.0155
-0.0751
-0.0615
-0.0372
-10.7327
-4.5033
4.2446
2
4.5672
0.4317
0.3216
3.1266
0.5003
5.6836
0.0194
0.4748
0.3663
-0.2735
0.057
0.2834
-0.0647
-0.2071
-0.0764
0.0179
0.0248
-0.0164
0.0027
0.0596
0.0565
-18.2209
2.1111
-0.4539
3
5.6911
1.4474
2.6499
1.8483
0.9121
2.8004
0.0173
0.1962
0.0156
-0.0602
0.024
0.2484
0.0739
-0.0298
-0.0413
-0.016
0.0113
0.0027
-0.0853
-0.0196
-0.0236
-23.2834
-10.1965
3.1229
4
11.2765
3.7803
-1.7954
4.4724
-1.302
2.6606
-0.1618
0.3469
-0.0322
-0.1828
0.0519
-0.3427
-0.0331
0.3486
0.11
0.0047
0.0286
-0.029
0.0549
-0.0229
-0.0443
0.7749
-6.0383
0.2859
5
3.8139
-1.6396
-0.457
2.5862
0.1535
3.7399
-0.1581
-0.4729
-0.5453
0.189
0.2059
0.0903
0.5707
0.2138
-0.0477
0.0828
0.0122
-0.0001
0.0385
0.0002
0.0548
-8.2958
-23.1426
26.4587
6
4.7778
0.0547
-0.9154
6.0458
2.0737
4.3924
-0.1304
-0.176
-0.2781
-0.2062
0.187
-0.1331
0.5143
0.2219
-0.0566
0.0935
0.0551
-0.0432
0.1402
0.0514
-0.0329
-2.4527
-24.5676
24.431
7
1.5759
-2.5394
-1.3095
9.0516
4.0802
2.3903
-0.1742
-0.0659
-0.3134
0.2166
0.1753
0.0793
0.2052
0.1436
-0.0011
0.029
0.0224
-0.0057
0.0178
-0.0207
-0.0171
-6.0226
-27.1051
13.9508
8
5.3033
-1.0376
-2.4661
6.9623
3.8539
7.8137
-0.0342
-0.5279
-0.0265
0.6094
0.0484
0.4936
0.1723
-0.2106
-0.0142
0.0682
-0.0008
0.018
0.0341
0.0338
0.0669
-19.9792
-17.6174
26.9443
9
5.4799
-0.3216
-0.0559
2.9125
0.6574
5.689
-0.038
0.3918
0.3623
-0.2818
-0.0831
0.4694
-0.2137
-0.9132
0.1211
0.0767
0.0916
-0.0251
0.2098
-0.1394
0.2327
-29.8435
13.7167
21.4772
10
9.6043
0.4875
-3.9615
5.6792
3.0383
11.1843
0.3607
-0.4416
2.0233
-1.4337
-0.2693
1.5131
-2.4049
-0.8567
-0.0915
0.5427
0.3901
-0.2206
0.4998
-0.1618
0.6983
-32.6873
24.2401
14.3296
11
5.3321
0.3554
0.0956
4.4214
1.9453
2.3947
0.0423
0.1485
0.4321
-0.5081
-0.059
0.252
-0.071
-0.1418
0.0167
-0.0172
0.056
0.021
0.085
-0.1478
0.146
-23.7063
11.9382
19.2977
12
3.1374
0.7166
0.3598
5.9219
-0.9192
4.8082
-0.0617
0.2156
0.6843
-0.1085
-0.1748
0.1011
-0.9808
-0.3975
0.2366
0.2474
0.1498
-0.0773
0.1373
-0.1342
0.3359
-24.5549
24.5274
21.4017
13
5.7372
-1.2603
0.3188
2.1506
0.7162
6.7417
-0.16
-1.1824
0.4366
0.2977
0.3592
-0.2236
-0.3275
0.8693
-0.1992
0.1307
-0.0654
0.0163
0.3879
-0.2252
0.1355
-4.0307
13.076
40.0078
14
13.2597
7.9747
9.2944
83.0042
-8.5597
18.3566
0.3276
1.0804
1.4534
-2.0985
0.2604
-0.1012
0.489
-1.0974
-0.5881
0.6341
0.1312
0.1466
0.7617
0.1766
0.5375
-1.0658
24.8432
47.0805
15
7.8066
-3.0355
3.0819
3.0563
-4.1115
5.7405
-0.5553
-1.2984
0.9869
0.9984
0.3834
-0.2001
-0.5227
-0.0889
0.1718
0.2902
0.0137
-0.0609
0.5397
-0.2421
0.1989
-9.8284
13.4568
47.2395
16
3.2301
-0.068
-0.0418
3.6285
0.8465
3.316
-0.095
-0.6786
0.9057
0.2979
0.213
-0.1184
-0.7099
0.3239
-0.118
0.2282
-0.0196
-0.0656
0.256
-0.2493
0.3366
-10.3262
20.4465
38.0961
17
77.3241
-41.7125
-60.2175
32.6209
42.4984
56.8056
-0.7737
-1.3747
1.2218
1.0835
1.1129
1.8878
0.6213
-0.0368
-0.3392
0.3644
-0.05
0.0068
0.374
0.1876
0.3371
-12.2818
14.4666
-8.6603
18
3.4232
-0.409
1.5092
1.858
-1.9255
4.8283
-0.0481
0.1393
-0.0528
0.1226
-0.0903
-0.2237
-0.3286
0.4375
0.1384
-0.0167
-0.0222
-0.0019
0.1595
0.0297
0.0265
8.8237
5.7842
-15.3515
19
4.2123
-0.4534
0.4988
2.4114
-1.9792
3.4148
0.152
0.0583
-0.0546
0.0717
-0.0764
-0.0348
0.1331
0.0578
-0.0756
-0.0708
-0.0256
-0.0128
0.0989
0.0297
-0.0191
-0.9511
5.1203
-17.4597
20
5.8301
-1.9509
-3.7716
4.9364
3.8839
13.8988
0.0554
-0.4646
0.8448
0.5901
0.1947
-0.1828
-0.8009
0.5077
-0.25
0.2288
-0.0882
-0.0563
0.1667
-0.003
0.1419
2.4739
16.6552
-12.9735
21
3.2467
-1.0093
1.7024
1.8264
-0.7207
5.2557
-0.0348
0.0977
0.128
-0.0087
-0.0296
0.0775
-0.4017
-0.7117
0.0644
0.0039
0.0456
0.053
0.3844
0.0353
-0.047
-18.98
13.1545
-33.3686
22
3.9495
-0.3858
2.1454
5.9312
-2.0778
5.2242
-0.22
0.0447
0.3024
0.3981
0.0589
0.2072
-0.5464
-0.4981
0.1611
0.0639
0.0617
0.0114
0.5113
0.0534
-0.0273
-19.6193
16.2952
-40.916
23
3.1044
-1.3413
1.4962
4.2951
-1.8469
7.0233
-0.132
0.2395
0.4284
-0.0655
-0.0667
-0.1103
-1.0174
-0.1592
0.1987
0.0432
0.0093
-0.0213
0.3263
0.0365
-0.0188
-11.2735
19.3723
-36.323
24
4.2981
5.6086
-0.7331
12.8211
-3.8021
6.3148
-0.133
-0.1803
0.4047
0.689
0.1637
0.1035
-1.1573
-0.4666
-0.0307
0.1748
0.1531
-0.0203
0.3714
-0.0075
0.0761
-16.1104
21.2426
-27.7969
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
0 - 34
2
X-RAY DIFFRACTION
2
A
35 - 78
3
X-RAY DIFFRACTION
3
A
79 - 141
4
X-RAY DIFFRACTION
4
A
142 - 167
5
X-RAY DIFFRACTION
5
B
0 - 55
6
X-RAY DIFFRACTION
6
B
56 - 81
7
X-RAY DIFFRACTION
7
B
82 - 140
8
X-RAY DIFFRACTION
8
B
141 - 164
9
X-RAY DIFFRACTION
9
C
0 - 46
10
X-RAY DIFFRACTION
10
C
47 - 62
11
X-RAY DIFFRACTION
11
C
63 - 104
12
X-RAY DIFFRACTION
12
C
105 - 163
13
X-RAY DIFFRACTION
13
D
0 - 48
14
X-RAY DIFFRACTION
14
D
49 - 63
15
X-RAY DIFFRACTION
15
D
64 - 90
16
X-RAY DIFFRACTION
16
D
91 - 163
17
X-RAY DIFFRACTION
17
E
-2 - 3
18
X-RAY DIFFRACTION
18
E
4 - 66
19
X-RAY DIFFRACTION
19
E
67 - 113
20
X-RAY DIFFRACTION
20
E
114 - 162
21
X-RAY DIFFRACTION
21
F
0 - 41
22
X-RAY DIFFRACTION
22
F
42 - 73
23
X-RAY DIFFRACTION
23
F
74 - 124
24
X-RAY DIFFRACTION
24
F
125 - 160
+
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