The sequence of this protein is not available at UNP database at the time of processing. Residues - ...The sequence of this protein is not available at UNP database at the time of processing. Residues -19 to 0 are expression tags.
Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.76 Å3/Da / Density % sol: 55.46 %
Crystal grow
Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 13%PEG2000MME, 50 mM Na-HEPES pH 7.0, 500 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 295K
-
Data collection
Diffraction
ID
Mean temperature (K)
Crystal-ID
1
100
1
2
100
1
1,2
1
Diffraction source
Source
Site
Beamline
ID
Wavelength (Å)
SYNCHROTRON
APS
24-ID-C
1
0.97925, 0.97941, 0.96403
SYNCHROTRON
APS
24-ID-C
2
1.28281
Radiation
ID
Protocol
Monochromatic (M) / Laue (L)
Scattering type
Wavelength-ID
1
MAD
M
x-ray
1
2
SINGLEWAVELENGTH
M
x-ray
2
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.97925
1
2
0.97941
1
3
0.96403
1
4
1.28281
1
Reflection
Redundancy: 6.9 % / Av σ(I) over netI: 13.4 / Number: 266945 / Rmerge(I) obs: 0.079 / Χ2: 1.02 / D res high: 3.2 Å / D res low: 50 Å / Num. obs: 38657 / % possible obs: 98.3
Diffraction reflection shell
Highest resolution (Å)
Lowest resolution (Å)
% possible obs (%)
ID
Rmerge(I) obs
Chi squared
Redundancy
6.89
50
99.3
1
0.055
1.024
7.1
5.47
6.89
100
1
0.079
1.025
7.1
4.78
5.47
100
1
0.077
1.027
7.3
4.34
4.78
100
1
0.067
1.002
7.3
4.03
4.34
100
1
0.077
1.003
7.3
3.79
4.03
100
1
0.105
1.018
7.4
3.6
3.79
100
1
0.134
1.018
7.3
3.45
3.6
99.9
1
0.186
1.022
7.1
3.31
3.45
98.2
1
0.261
1.031
6
3.2
3.31
85.9
1
0.305
1.019
4.9
Reflection
Resolution: 3.2→50 Å / Num. obs: 38657 / % possible obs: 98.3 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.079 / Χ2: 1.019 / Net I/σ(I): 13.4
Method to determine structure: MAD / Resolution: 3.2→50 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.888 / SU B: 59.032 / SU ML: 0.486 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.617 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The data were collected from 2 crystals. One crystal was used for Se MAD, and the other one for Zn SAD. The Se MAD data was used for ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The data were collected from 2 crystals. One crystal was used for Se MAD, and the other one for Zn SAD. The Se MAD data was used for phasing/structure determination. The Zn data was used solelly to determine the Zn sites
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.292
3880
10 %
RANDOM
Rwork
0.253
-
-
-
obs
0.257
34862
98.51 %
-
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: 68.793 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-4.56 Å2
0 Å2
2.36 Å2
2-
-
3.03 Å2
0 Å2
3-
-
-
3.05 Å2
Refinement step
Cycle: LAST / Resolution: 3.2→50 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
13868
0
114
4
13986
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.007
0.022
14228
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
9844
X-RAY DIFFRACTION
r_angle_refined_deg
1.247
1.993
19261
X-RAY DIFFRACTION
r_angle_other_deg
0.87
3
23962
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
2.24
5
1772
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
24.383
23.598
642
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
11.071
15
2511
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
10.925
15
126
X-RAY DIFFRACTION
r_chiral_restr
0.069
0.2
2166
X-RAY DIFFRACTION
r_gen_planes_refined
0.003
0.02
15758
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
2816
X-RAY DIFFRACTION
r_nbd_refined
0.201
0.2
3530
X-RAY DIFFRACTION
r_nbd_other
0.18
0.2
10655
X-RAY DIFFRACTION
r_nbtor_refined
0.169
0.2
7069
X-RAY DIFFRACTION
r_nbtor_other
0.08
0.2
7148
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.13
0.2
272
X-RAY DIFFRACTION
r_xyhbond_nbd_other
0.169
0.2
2
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.128
0.2
16
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.18
0.2
94
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.197
0.2
2
X-RAY DIFFRACTION
r_mcbond_it
0.329
1.5
11191
X-RAY DIFFRACTION
r_mcbond_other
0.031
1.5
3628
X-RAY DIFFRACTION
r_mcangle_it
0.364
2
14212
X-RAY DIFFRACTION
r_scbond_it
0.422
3
6036
X-RAY DIFFRACTION
r_scangle_it
0.699
4.5
5049
Refine LS restraints NCS
Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION
Ens-ID
Dom-ID
Number
Type
Rms dev position (Å)
Weight position
1
1
4095
MEDIUMPOSITIONAL
0.27
0.5
1
1
5116
LOOSEPOSITIONAL
0.36
5
1
1
4095
MEDIUMTHERMAL
0.75
2
1
1
5116
LOOSETHERMAL
0.8
10
2
3
401
MEDIUMPOSITIONAL
0.17
0.5
2
3
508
LOOSEPOSITIONAL
0.3
5
2
3
401
MEDIUMTHERMAL
0.13
2
2
3
508
LOOSETHERMAL
0.14
10
3
5
603
MEDIUMPOSITIONAL
0.2
0.5
3
5
893
LOOSEPOSITIONAL
0.3
5
3
5
603
MEDIUMTHERMAL
0.13
2
3
5
893
LOOSETHERMAL
0.11
10
LS refinement shell
Resolution: 3.2→3.284 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.368
256
-
Rwork
0.338
2172
-
all
-
2428
-
obs
-
-
83.61 %
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
2.5211
0.1624
0.0578
2.0941
-0.1611
1.1308
0.1344
0.0424
0.0415
0.1447
-0.1369
-0.0461
-0.0346
0.0897
0.0025
-0.1945
-0.0434
0.0144
-0.2036
-0.1061
-0.3628
47.6592
15.069
24.2715
2
2.5418
0.7188
0.0269
2.8011
0.6631
1.2486
0.222
-0.1165
0.122
0.1334
-0.4007
0.4936
-0.0463
-0.3965
0.1786
-0.1508
0.0418
-0.0196
0.0188
-0.0813
-0.0581
11.1944
49.2698
23.3983
3
16.9653
-1.7694
2.5102
2.9193
-0.5533
0.4025
0.1302
0.2724
-1.0262
0.0843
-0.0212
0.2549
-0.1977
-0.0598
-0.109
0.062
0.0641
-0.027
0.3452
-0.0093
0.4236
-11.6142
-2.4702
32.2518
4
11.824
-2.3753
-0.2107
0.4772
0.0423
0.0038
-0.124
0.3393
-0.8198
-0.7355
0.2515
-0.3148
0.0477
0.6711
-0.1275
0.5116
-0.0814
0.2591
0.5319
-0.1996
1.3057
72.3835
65.9044
29.0911
5
7.3027
0.9021
1.1911
7.4569
-2.1711
10.3377
-0.1463
-0.7026
-1.2386
0.931
-0.0208
-1.0159
0.5023
0.1466
0.1671
0.6494
0.0114
0.0121
0.4156
0.1916
0.3197
45.5916
-6.5832
60.9701
6
6.1914
-3.7778
-2.3961
10.9468
1.849
5.586
-0.3093
0.6481
-0.4834
-0.1711
0.0282
0.52
0.5928
-0.3196
0.2811
0.4426
-0.0356
0.0417
0.4875
0.1324
0.0031
10.7051
68.2578
60.5656
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
1 - 117
21 - 137
2
X-RAY DIFFRACTION
1
A
A
256 - 286
276 - 306
3
X-RAY DIFFRACTION
1
A
A
399 - 949
419 - 969
4
X-RAY DIFFRACTION
2
B
B
1 - 117
21 - 137
5
X-RAY DIFFRACTION
2
B
B
256 - 286
276 - 306
6
X-RAY DIFFRACTION
2
B
B
399 - 949
419 - 969
7
X-RAY DIFFRACTION
3
A
A
118 - 153
138 - 173
8
X-RAY DIFFRACTION
3
A
A
200 - 255
220 - 275
9
X-RAY DIFFRACTION
4
B
B
118 - 151
138 - 171
10
X-RAY DIFFRACTION
4
B
B
205 - 229
225 - 249
11
X-RAY DIFFRACTION
5
A
A
287 - 309
307 - 329
12
X-RAY DIFFRACTION
5
A
A
314 - 318
334 - 338
13
X-RAY DIFFRACTION
5
A
A
324 - 398
344 - 418
14
X-RAY DIFFRACTION
6
B
B
287 - 398
307 - 418
+
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