Mass: 18.015 Da / Num. of mol.: 415 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THIS CONSTRUCT IS COMPRISED OF RESIDUES 28-419 OF THE FULL-LENGTH PROTEIN. IT WAS EXPRESSED WITH A ...THIS CONSTRUCT IS COMPRISED OF RESIDUES 28-419 OF THE FULL-LENGTH PROTEIN. IT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.12 Å3/Da / Density % sol: 42.08 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: NANODROP, 20.0% PEG 3000, 0.1M Citrate pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution: 1.85→29.604 Å / Num. obs: 66845 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 9.4
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
1.85-1.9
3.8
0.67
1.9
18642
4946
0.67
100
1.9-1.95
3.8
0.581
2.2
18011
4776
0.581
100
1.95-2.01
3.8
0.456
2.8
17666
4681
0.456
100
2.01-2.07
3.8
0.36
3.4
17160
4538
0.36
100
2.07-2.14
3.8
0.303
4.1
16615
4382
0.303
100
2.14-2.21
3.8
0.251
4.9
16185
4267
0.251
100
2.21-2.29
3.8
0.207
5.8
15497
4096
0.207
100
2.29-2.39
3.8
0.173
6.8
15011
3952
0.173
100
2.39-2.49
3.8
0.151
7.7
14513
3819
0.151
100
2.49-2.62
3.8
0.124
9.4
13739
3616
0.124
100
2.62-2.76
3.8
0.107
11.1
13096
3441
0.107
100
2.76-2.93
3.8
0.096
12.5
12360
3246
0.096
100
2.93-3.13
3.8
0.076
15
11763
3095
0.076
100
3.13-3.38
3.8
0.065
17.3
10866
2870
0.065
100
3.38-3.7
3.8
0.056
19.7
10010
2647
0.056
100
3.7-4.14
3.8
0.049
21.8
9002
2389
0.049
100
4.14-4.78
3.8
0.052
23.5
7945
2113
0.052
100
4.78-5.85
3.7
0.053
24.6
6655
1784
0.053
100
5.85-8.27
3.7
0.046
25.5
5202
1413
0.046
100
8.27-29.604
3.6
0.043
26.6
2754
774
0.043
97.8
-
Phasing
Phasing
Method: MAD
-
Processing
Software
Name
Version
Classification
NB
REFMAC
5.5.0053
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
SCALA
3.2.5
datascaling
PDB_EXTRACT
3.006
dataextraction
MAR345
CCD
datacollection
MOSFLM
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.85→29.604 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 7.77 / SU ML: 0.1 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.126 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. ELECTRON DENSITY INDICATES THAT THE PEPTIDE BOND BETWEEN CYS 332 AND TRP 333 IN BOTH SUBUNITS IN THE ASYMMETRIC UNIT IS IN THE CIS-CONFIGURATION. THIS IS IN THE VICINITY OF THE PUTATIVE ACTIVE SITE. 5. 1,2-ETHANEDIOL (EDO) FROM THE CRYOPROTECTION CONDITION HAS BEEN MODELED IN THE SOLVENT STRUCTURE.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.205
3384
5.1 %
RANDOM
Rwork
0.169
-
-
-
obs
0.171
66817
99.97 %
-
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