Resolution: 1.7→29.617 Å / Num. obs: 49360 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 20.28 % / Biso Wilson estimate: 23.322 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.56
Reflection shell
Resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
1.7-1.76
1.292
1.79
72693
8745
1
98.3
1.76-1.83
1.028
2.8
97236
8912
1
99.6
1.83-1.91
0.731
4
98242
8647
1
99.7
1.91-2.02
0.469
6
112416
9826
1
99.6
2.02-2.14
0.295
8.9
97340
8483
1
99.8
2.14-2.31
0.21
11.8
106846
9267
1
99.9
2.31-2.54
0.157
15.1
102007
8824
1
99.9
2.54-2.9
0.111
20.1
102780
8867
1
99.9
2.9-3.66
0.073
28.5
106156
9127
1
99.9
3.66-29.62
0.058
36
105151
9063
1
99.6
-
Phasing
Phasing
Method: MAD
-
Processing
Software
Name
Version
Classification
NB
REFMAC
5.5.0053
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
XSCALE
datascaling
PDB_EXTRACT
3.006
dataextraction
XDS
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.7→29.617 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.969 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.394 / SU ML: 0.049 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.078 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. PLP IS COVALENTLY ATTACHED TO LYS187 (LLP). RESIDUAL DENSITY SUGGESTS ADDITIONAL MOIETY MAY BE ATTACHED TO THE C4A ATOM OF PLP. THESE DENSITIES ARE MODELED AS AN UNKNOWN LIGAND (UNL). 5. GLYCEROL MODELED ARE PRESENT IN CRYO CONDITION.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.167
2495
5.1 %
RANDOM
Rwork
0.147
-
-
-
obs
0.148
49180
99.68 %
-
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