Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.3 Å3/Da / Density % sol: 46.45 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.5 uL protein (mixed 1:700 w/w chymotrypsin:protein before setup) + 0.5 uL well solution (16% w/v PEG 8000, 0.04 M potassium phosphate monobasic, 20% v/v glycerol) + 0.1 uL 40% formamide ...Details: 0.5 uL protein (mixed 1:700 w/w chymotrypsin:protein before setup) + 0.5 uL well solution (16% w/v PEG 8000, 0.04 M potassium phosphate monobasic, 20% v/v glycerol) + 0.1 uL 40% formamide (4% final concentration), VAPOR DIFFUSION, SITTING DROP, temperature 293K
Redundancy: 16.1 % / Number: 327384 / Rmerge(I) obs: 0.047 / Χ2: 1.05 / D res high: 1.64 Å / D res low: 50 Å / Num. obs: 20328 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)
Lowest resolution (Å)
ID
Rmerge(I) obs
Chi squared
Redundancy
4.45
50
1
0.025
1.155
14.8
3.53
4.45
1
0.028
1.476
16.3
3.09
3.53
1
0.03
1.509
16.4
2.8
3.09
1
0.037
1.335
16.5
2.6
2.8
1
0.047
1.197
16.5
2.45
2.6
1
0.055
1.12
16.5
2.33
2.45
1
0.067
1.077
16.4
2.23
2.33
1
0.078
1.152
16.4
2.14
2.23
1
0.092
1.076
16.4
2.07
2.14
1
0.102
1.067
16.3
2
2.07
1
0.132
1.044
16.2
1.94
2
1
0.158
1.011
16.1
1.89
1.94
1
0.181
0.97
16.1
1.85
1.89
1
0.24
0.912
16.1
1.81
1.85
1
0.307
0.849
16
1.77
1.81
1
0.358
0.808
16
1.73
1.77
1
0.44
0.819
15.9
1.7
1.73
1
0.553
0.812
15.8
1.67
1.7
1
0.643
0.786
15.7
1.64
1.67
1
0.775
0.774
15.8
Reflection
Resolution: 1.64→50 Å / Num. obs: 20404 / % possible obs: 99.9 % / Redundancy: 27.8 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.056 / Χ2: 1.08 / Net I/σ(I): 80.4
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Num. unique all
Χ2
Diffraction-ID
% possible all
1.64-1.67
27.2
0.864
1004
0.671
1
100
1.67-1.7
27.1
0.727
1020
0.693
1
100
1.7-1.73
27.3
0.616
1008
0.721
1
100
1.73-1.77
27.4
0.504
1009
0.735
1
100
1.77-1.81
27.5
0.413
996
0.754
1
100
1.81-1.85
27.6
0.349
1022
0.787
1
100
1.85-1.89
27.7
0.274
1004
0.843
1
100
1.89-1.94
27.8
0.212
1013
0.908
1
100
1.94-2
27.9
0.18
1000
0.952
1
100
2-2.07
28
0.151
1020
0.996
1
100
2.07-2.14
28
0.12
1024
1.053
1
100
2.14-2.23
28.3
0.108
1015
1.105
1
100
2.23-2.33
28.3
0.092
1024
1.165
1
100
2.33-2.45
28.4
0.081
1012
1.134
1
100
2.45-2.6
28.5
0.067
1014
1.209
1
100
2.6-2.8
28.5
0.057
1036
1.275
1
100
2.8-3.09
28.5
0.046
1020
1.479
1
100
3.09-3.53
28.3
0.038
1041
1.762
1
100
3.53-4.45
28.2
0.033
1048
1.758
1
100
4.45-50
25.6
0.029
1074
1.475
1
98.6
-
Processing
Software
Name
Version
Classification
NB
SCALEPACK
datascaling
REFMAC
5.8.0073
refinement
PDB_EXTRACT
3.14
dataextraction
SBC-Collect
datacollection
HKL-3000
datareduction
HKL-3000
datascaling
SOLVE
2 .13
phasing
RESOLVE
2 .13
phasing
Coot
0.7.2
modelbuilding
ARP/wARP
7.4.0
modelbuilding
Refinement
Method to determine structure: SAD / Resolution: 1.64→50 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.693 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2123
637
3.2 %
RANDOM
Rwork
0.1698
-
-
-
obs
0.1711
20208
99.06 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
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