Mass: 18.015 Da / Num. of mol.: 598 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT 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: 2
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
0.978791
1
2
0.91837
1
3
0.97956
1
Reflection
Resolution: 1.7→29.748 Å / Num. obs: 120878 / % possible obs: 99.9 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 4.6
Reflection shell
Diffraction-ID: 2
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
1.7-1.74
3.8
0.772
1
32645
8703
0.772
99.3
1.74-1.79
7.4
0.748
1
63583
8631
0.748
100
1.79-1.84
10.8
0.674
1.1
91114
8401
0.674
100
1.84-1.9
10.8
0.484
1.5
88695
8179
0.484
100
1.9-1.96
10.8
0.345
2.2
85606
7895
0.345
100
1.96-2.03
10.8
0.25
3
83243
7681
0.25
100
2.03-2.11
10.8
0.202
3.7
80451
7435
0.202
100
2.11-2.19
10.8
0.169
4.3
77158
7124
0.169
100
2.19-2.29
10.8
0.149
4.8
73895
6848
0.149
100
2.29-2.4
10.8
0.132
5.4
70812
6571
0.132
100
2.4-2.53
10.7
0.118
6
67231
6262
0.118
100
2.53-2.69
10.7
0.105
6.6
63327
5917
0.105
100
2.69-2.87
10.6
0.089
7.7
59299
5569
0.089
100
2.87-3.1
10.6
0.08
8.5
55139
5216
0.08
100
3.1-3.4
10.5
0.08
8.2
50605
4815
0.08
100
3.4-3.8
10.2
0.083
7.9
44413
4372
0.083
100
3.8-4.39
9.6
0.082
7.9
37402
3877
0.082
100
4.39-5.38
10.1
0.069
9.2
33184
3295
0.069
100
5.38-7.6
10.7
0.067
9.8
27971
2616
0.067
100
7.6-29.76
9.6
0.061
10.5
14140
1471
0.061
97.3
-
Phasing
Phasing
Method: MAD
-
Processing
Software
Name
Version
Classification
NB
SHELXL-97
refinement
PHENIX
refinement
SHELX
phasing
SHELX
refinement
SCALA
datascaling
PDB_EXTRACT
3.004
dataextraction
MOSFLM
datareduction
SHELXD
phasing
autoSHARP
phasing
MolProbity
3beta29
modelbuilding
Refinement
Method to determine structure: MAD / Resolution: 1.7→29.748 Å / Num. parameters: 34792 / Num. restraintsaints: 62193 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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. 3. GLYCEROL MOLECULES FROM THE CRYSTALLIZATION SOLUTION ARE MODELED. 4. THE DIFFRACTION DATA IS TWINNED WITH THE TWINNING OPERATOR "-H,-K,L" AND THE REFINED TWIN FRACTION IS 0.407.
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