Mass: 18.015 Da / Num. of mol.: 418 / 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: 2.7 Å3/Da / Density % sol: 52 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, hanging drop Details: PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, 0.005 M BisTris PH 7.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (7% PEG 4K, 0.40 M ...Details: PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, 0.005 M BisTris PH 7.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (7% PEG 4K, 0.40 M sodium chloride, 0.1 M MES/Acetate pH 5.5) CRYOPROTECTED WITH 10% PEG 4K, 0.1 M MES/Acetate pH 5.5, 25% Ethylene glycol, vapor diffusion, hanging drop, temperature 293K
Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 4, 2006 Details: HORIZONTAL SAGITALLY FOCUSING SECOND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR
Radiation
Monochromator: CRYOGENICALLY COOLED SI (220) DOUBLE BOUNCE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97925 Å / Relative weight: 1
Reflection
Resolution: 1.92→40.612 Å / Num. obs: 39789 / % possible obs: 97.5 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.074 / Χ2: 1.458 / Net I/σ(I): 13.377
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. unique all
Χ2
% possible all
1.92-1.99
5.4
0.245
5.769
3895
1.233
95.5
1.99-2.07
6.3
0.222
3915
1.234
97
2.07-2.16
6.5
0.167
3931
1.222
96.9
2.16-2.28
6.4
0.136
3943
1.189
97
2.28-2.42
6.5
0.117
3904
1.296
96.4
2.42-2.61
6.5
0.105
3881
1.413
96.6
2.61-2.87
6.4
0.089
3975
1.438
97.3
2.87-3.28
6.5
0.069
3992
1.711
98.1
3.28-4.14
6.5
0.057
4133
1.595
99.6
4.14-40.61
7.1
0.054
4220
2.062
100
-
Phasing
Phasing
Method: SAD
Phasing MAD set
R cullis centric: 0 / Highest resolution: 1.92 Å / Lowest resolution: 39.72 Å / Power centric: 0
ID
R cullis acentric
Power acentric
Reflection acentric
Reflection centric
ISO_1
0
0
37124
2624
ANO_1
0.644
1.739
36468
0
Phasing MAD set shell
R cullis centric: 0 / Power centric: 0
ID
Resolution (Å)
R cullis acentric
Power acentric
Reflection acentric
Reflection centric
ISO_1
8.4-39.72
0
0
392
136
ISO_1
6.01-8.4
0
0
755
141
ISO_1
4.92-6.01
0
0
993
145
ISO_1
4.27-4.92
0
0
1167
133
ISO_1
3.83-4.27
0
0
1317
136
ISO_1
3.5-3.83
0
0
1488
139
ISO_1
3.24-3.5
0
0
1600
132
ISO_1
3.03-3.24
0
0
1735
131
ISO_1
2.86-3.03
0
0
1800
124
ISO_1
2.71-2.86
0
0
1930
120
ISO_1
2.59-2.71
0
0
2015
118
ISO_1
2.48-2.59
0
0
2132
134
ISO_1
2.38-2.48
0
0
2168
128
ISO_1
2.29-2.38
0
0
2264
121
ISO_1
2.22-2.29
0
0
2402
130
ISO_1
2.15-2.22
0
0
2403
129
ISO_1
2.08-2.15
0
0
2531
127
ISO_1
2.02-2.08
0
0
2615
136
ISO_1
1.97-2.02
0
0
2704
129
ISO_1
1.92-1.97
0
0
2713
135
ANO_1
8.4-39.72
0.494
2.425
392
0
ANO_1
6.01-8.4
0.347
3.797
755
0
ANO_1
4.92-6.01
0.411
3.227
993
0
ANO_1
4.27-4.92
0.531
2.408
1166
0
ANO_1
3.83-4.27
0.569
2.224
1311
0
ANO_1
3.5-3.83
0.536
2.227
1466
0
ANO_1
3.24-3.5
0.543
2.244
1570
0
ANO_1
3.03-3.24
0.548
2.308
1694
0
ANO_1
2.86-3.03
0.533
2.337
1758
0
ANO_1
2.71-2.86
0.597
2.065
1881
0
ANO_1
2.59-2.71
0.598
1.934
1965
0
ANO_1
2.48-2.59
0.632
1.722
2094
0
ANO_1
2.38-2.48
0.661
1.598
2142
0
ANO_1
2.29-2.38
0.71
1.456
2237
0
ANO_1
2.22-2.29
0.771
1.232
2363
0
ANO_1
2.15-2.22
0.786
1.205
2369
0
ANO_1
2.08-2.15
0.803
1.08
2507
0
ANO_1
2.02-2.08
0.844
0.96
2590
0
ANO_1
1.97-2.02
0.852
0.862
2647
0
ANO_1
1.92-1.97
0.896
0.739
2568
0
Phasing MAD set site
ID
Cartn x (Å)
Cartn y (Å)
Cartn z (Å)
Atom type symbol
B iso
Occupancy
1
103.773
-18.099
18.977
SE
24.28
1.19
2
42.959
-23.549
17.219
SE
20
1.16
3
121.967
15.611
1.601
SE
19.37
1.07
4
133.903
-20.756
16.55
SE
26.22
1.01
5
53.422
-6.207
17.148
SE
35.01
1.01
6
26.294
-5
15.713
SE
32.81
0.92
7
125.342
14.378
12.89
SE
14.21
0.68
8
46.369
6.024
15.967
SE
18.39
0.64
9
49.154
-1.535
15.586
SE
15.97
0.55
10
128.011
13.934
20.482
SE
13.12
0.35
11
43.99
5.391
18.714
SE
14.72
0.44
12
122.906
-23.911
13.509
SE
11.6
0.37
13
128.859
8.436
15.017
SE
19.61
0.33
14
49.87
3.954
10.12
SE
17.85
0.24
15
128.939
9.09
18.781
SE
22.42
0.13
16
59.389
-25.674
8.552
SE
22.42
0.06
17
108.99
20.09
29.395
SE
27.2
0.22
18
48.672
1.445
10.151
SE
20.2
0.11
19
112.306
2.563
21.624
SE
20.2
0.1
Phasing dm
Method: Solvent flattening and Histogram matching / Reflection: 39747
Phasing dm shell
Resolution (Å)
Delta phi final
FOM
Reflection
8.58-100
66.3
0.764
507
6.62-8.58
62.6
0.898
567
5.59-6.62
56.6
0.894
699
4.92-5.59
57.5
0.926
794
4.45-4.92
53.5
0.935
844
4.09-4.45
59.4
0.939
935
3.81-4.09
56.4
0.934
1042
3.58-3.81
57.8
0.92
1116
3.38-3.58
59.7
0.928
1122
3.22-3.38
57.5
0.915
1225
3.07-3.22
59.5
0.929
1257
2.95-3.07
57.4
0.913
1277
2.84-2.95
57.7
0.92
1390
2.74-2.84
57.9
0.916
1348
2.65-2.74
58.7
0.917
1480
2.56-2.65
59.4
0.916
1457
2.49-2.56
58
0.915
1553
2.42-2.49
59.6
0.911
1510
2.36-2.42
60.3
0.915
1659
2.3-2.36
59.9
0.912
1609
2.25-2.3
63.3
0.902
1697
2.2-2.25
61.7
0.912
1739
2.15-2.2
64.7
0.91
1742
2.1-2.15
63.5
0.902
1849
2.06-2.1
68.1
0.893
1799
2.02-2.06
69.2
0.875
1883
1.99-2.02
69
0.869
1920
1.92-1.99
73.2
0.805
3727
-
Processing
Software
Name
Version
Classification
NB
HKL
dataprocessing
SHARP
phasing
DM
5
phasing
REFMAC
5.2.0005
refinement
PDB_EXTRACT
2
dataextraction
HKL-2000
datareduction
HKL
datascaling
PHENIX
(HYSS)
phasing
ARP/wARP
modelbuilding
Refinement
Method to determine structure: SAD / Resolution: 1.92→40.612 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.255 / WRfactor Rwork: 0.207 / SU B: 6.887 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.157 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.235
1998
5.024 %
RANDOM
Rwork
0.19
-
-
-
all
0.192
-
-
-
obs
0.192
39773
97.423 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
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