Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O
-
Details
Sequence details
THE N-TERMINAL 36 AMINO ACIDS OF THE PROTEIN WERE NOT VISIBLE IN THE ELECTRON DENSITY. PROTEIN ...THE N-TERMINAL 36 AMINO ACIDS OF THE PROTEIN WERE NOT VISIBLE IN THE ELECTRON DENSITY. PROTEIN SEQUENCE ANALYSIS OF A REDISSOLVED CRYSTAL CONFIRMED THE PRESENCE OF THE N-TERMINUS IN THE CRYSTALS. THE CONCLUSION IS THEN THAT THE N-TERMINAL 36 AMINO ACIDS ARE DISORDERED.
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.41 Å3/Da / Density % sol: 48.9 %
Crystal grow
pH: 6 Details: PROTEIN WAS CRYSTALLISED FROM 50MM SUCCINATE, PH 6.0, 10MM HEPES PH 7.0, 18% PEG 4000, 1% N-OCTYLGLUCOSIDE
Resolution: 2→40 Å / Num. obs: 29479 / % possible obs: 90 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 23.6 Å2 / Rsym value: 0.032 / Net I/σ(I): 21.6
Reflection shell
Resolution: 2→2.05 Å / Redundancy: 1.56 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.281 / % possible all: 60.6
Reflection
*PLUS
Lowest resolution: 20 Å / Rmerge(I) obs: 0.032
-
Processing
Software
Name
Version
Classification
X-PLOR
3.1
modelbuilding
X-PLOR
3.1
refinement
DENZO
datareduction
SCALEPACK
datascaling
X-PLOR
3.1
phasing
Refinement
Method to determine structure: MIR / Resolution: 2→6 Å / Rfactor Rfree error: 0.0046 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0 / σ(F): 1
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.25
2918
10 %
RANDOM
Rwork
0.183
-
-
-
obs
0.183
29479
85.6 %
-
Displacement parameters
Biso mean: 31.8 Å2
Refine analyze
Luzzati coordinate error obs: 0.29 Å / Luzzati d res low obs: 4 Å / Luzzati sigma a obs: 0.29 Å
Refinement step
Cycle: LAST / Resolution: 2→6 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3506
0
48
319
3873
Refine LS restraints
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
x_bond_d
0.01
X-RAY DIFFRACTION
x_bond_d_na
X-RAY DIFFRACTION
x_bond_d_prot
X-RAY DIFFRACTION
x_angle_d
X-RAY DIFFRACTION
x_angle_d_na
X-RAY DIFFRACTION
x_angle_d_prot
X-RAY DIFFRACTION
x_angle_deg
1.55
X-RAY DIFFRACTION
x_angle_deg_na
X-RAY DIFFRACTION
x_angle_deg_prot
X-RAY DIFFRACTION
x_dihedral_angle_d
22.8
X-RAY DIFFRACTION
x_dihedral_angle_d_na
X-RAY DIFFRACTION
x_dihedral_angle_d_prot
X-RAY DIFFRACTION
x_improper_angle_d
1.43
X-RAY DIFFRACTION
x_improper_angle_d_na
X-RAY DIFFRACTION
x_improper_angle_d_prot
X-RAY DIFFRACTION
x_mcbond_it
X-RAY DIFFRACTION
x_mcangle_it
X-RAY DIFFRACTION
x_scbond_it
X-RAY DIFFRACTION
x_scangle_it
LS refinement shell
Resolution: 2→2.09 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 8
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