Mass: 18.015 Da / Num. of mol.: 633 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THE CONSTRUCT (RESIDUE 23-520) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUE 23-520) 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: 2.62 Å3/Da / Density % sol: 53.09 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 30.0000% PEG-6000, 0.1M HEPES pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 13, 2008 / Details: Flat mirror (vertical focusing)
Radiation
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
0.91162
1
2
0.97871
1
3
0.97799
1
Reflection
Resolution: 1.75→29.553 Å / Num. obs: 58982 / % possible obs: 99.9 % / Redundancy: 4.1 % / Biso Wilson estimate: 21.042 Å2 / Rmerge(I) obs: 0.118 / Rsym value: 0.118 / Net I/σ(I): 4.449
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
1.75-1.8
4.1
0.686
1.1
17876
4336
0.686
100
1.8-1.84
4.1
0.574
1.3
17219
4174
0.574
100
1.84-1.9
4.1
0.506
1.5
16952
4112
0.506
100
1.9-1.96
4.1
0.416
1.7
16428
3979
0.416
100
1.96-2.02
4.1
0.348
2.1
15934
3869
0.348
100
2.02-2.09
4.1
0.289
2.4
15384
3741
0.289
100
2.09-2.17
4.1
0.251
2.8
14914
3625
0.251
100
2.17-2.26
4.1
0.213
3.2
14278
3473
0.213
100
2.26-2.36
4.1
0.184
3.6
13629
3320
0.184
100
2.36-2.47
4.1
0.162
4.2
13184
3219
0.162
100
2.47-2.61
4.1
0.142
4.8
12500
3042
0.142
100
2.61-2.77
4.1
0.125
5.2
11820
2880
0.125
100
2.77-2.96
4.1
0.105
6.2
11192
2728
0.105
100
2.96-3.2
4.1
0.09
6.9
10443
2556
0.09
100
3.2-3.5
4.1
0.076
8.3
9479
2330
0.076
100
3.5-3.91
4.1
0.069
8.5
8704
2130
0.069
100
3.91-4.52
4
0.071
8
7593
1890
0.071
100
4.52-5.53
4
0.081
7.6
6445
1613
0.081
99.8
5.53-7.83
4
0.078
7.8
4977
1256
0.078
99.4
7.83-29.553
3.8
0.061
9.6
2685
709
0.061
96.9
-
Phasing
Phasing
Method: MAD
-
Processing
Software
Name
Version
Classification
NB
REFMAC
5.4.0067
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
SCALA
3.2.5
datascaling
PDB_EXTRACT
3.006
dataextraction
MOSFLM
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.75→29.553 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 4.864 / SU ML: 0.078 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.094 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. RAMACHANDRAN OUTLIER RESIDUE 330 IS SUPPORTED BY DENSITY. 5. PEG-200 MOLECULE FROM THE CRYO SOLUTION IS MODELED.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.189
2984
5.1 %
RANDOM
Rwork
0.158
-
-
-
obs
0.159
58982
99.89 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH 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