Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THE CONSTRUCT (RESIDUES 1-161) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 1-161) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE FOLLOWED BY THE TARGET SEQUENCE.
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.36 Å3/Da / Density % sol: 47.86 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.2000M Na2HPO4, 20.0000% PEG-3350, No Buffer pH 4.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Monochromator: Single crystal Si(111) bent monochromator (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.91837
1
2
0.97959
1
3
0.97886
1
Reflection
Resolution: 1.95→28.307 Å / Num. obs: 12340 / % possible obs: 97.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 22.604 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 10.9
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
1.95-2
2.8
0.691
1
2023
729
0.691
80.2
2-2.06
3
0.483
1.5
2412
799
0.483
91
2.06-2.12
3.5
0.373
1.9
3101
894
0.373
98.8
2.12-2.18
3.7
0.339
2.1
3085
831
0.339
100
2.18-2.25
3.7
0.269
2.6
3054
833
0.269
100
2.25-2.33
3.7
0.247
3
2994
807
0.247
100
2.33-2.42
3.7
0.209
3.4
2829
771
0.209
100
2.42-2.52
3.7
0.173
4.2
2736
743
0.173
100
2.52-2.63
3.7
0.151
4.8
2628
711
0.151
100
2.63-2.76
3.7
0.128
5.5
2516
682
0.128
100
2.76-2.91
3.7
0.1
6.8
2459
668
0.1
100
2.91-3.08
3.7
0.082
9
2232
605
0.082
100
3.08-3.3
3.7
0.064
10.9
2129
579
0.064
100
3.3-3.56
3.7
0.054
12.5
2054
560
0.054
100
3.56-3.9
3.7
0.051
12.7
1783
488
0.051
100
3.9-4.36
3.7
0.047
13.2
1711
465
0.047
100
4.36-5.03
3.6
0.042
15.7
1461
401
0.042
100
5.03-6.17
3.6
0.054
12.4
1245
347
0.054
100
6.17-8.72
3.5
0.042
15.5
954
273
0.042
100
8.72-28.31
3.3
0.031
20.3
508
154
0.031
98
-
Phasing
Phasing
Method: MAD
-
Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0019
refinement
PHENIX
refinement
SOLVE
phasing
MolProbity
3beta29
modelbuilding
SCALA
3.2.5
datascaling
PDB_EXTRACT
3.006
dataextraction
MOSFLM
datareduction
Refinement
Method to determine structure: MAD / Resolution: 1.95→28.307 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.928 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 6.888 / SU ML: 0.104 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.148 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: (1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2). ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. (3). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING ...Details: (1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2). ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. (3). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. (4). RAMACHANDRAN OUTLIER OF RESIDUE GLY59 IS SUPPORTED BY ELECTRON DENSITY. (5). RESIDUES 102-105 WERE NOT MODELED DUE TO POOR ELECTRON DENSITY IN THIS REGION. (6). DIMETHYL SULFOXIDE (DMS) MOLECULES FROM THE CRYSTALLIZATION BUFFERS WERE MODELED INTO THE STRUCTURE.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.218
599
4.9 %
RANDOM
Rwork
0.172
-
-
-
obs
0.174
12306
97.45 %
-
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