Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97926 Å / Relative weight: 1
Reflection
Resolution: 2.188→47.193 Å / Num. obs: 9987 / % possible obs: 99.4 % / Redundancy: 6.2 % / Biso Wilson estimate: 41.97 Å2 / Rpim(I) all: 0.034 / Rrim(I) all: 0.084 / Rsym value: 0.076 / Net I/av σ(I): 5.7 / Net I/σ(I): 11.4 / Num. measured all: 62270
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique obs
Rpim(I) all
Rrim(I) all
Rsym value
Net I/σ(I) obs
% possible all
2.19-2.31
6.1
0.643
1.1
8294
1368
0.278
0.702
0.643
3
96.1
2.31-2.45
6.2
0.448
1.5
8497
1361
0.197
0.49
0.448
4.4
100
2.45-2.61
6.5
0.268
2.4
8364
1283
0.115
0.292
0.268
6
100
2.61-2.82
6.2
0.17
3.9
7382
1185
0.074
0.185
0.17
7.2
100
2.82-3.09
6.4
0.105
6.4
7106
1103
0.045
0.114
0.105
10.3
100
3.09-3.46
6.4
0.079
8.3
6464
1015
0.034
0.086
0.079
13.6
100
3.46-3.99
6.2
0.064
9.5
5586
900
0.028
0.07
0.064
20.5
100
3.99-4.89
6.2
0.052
11.6
4823
784
0.023
0.057
0.052
25.1
100
4.89-6.92
6.1
0.053
11.2
3701
609
0.024
0.058
0.053
21.8
100
6.92-47.193
5.4
0.043
10.4
2053
379
0.02
0.047
0.043
28.6
99.8
-
Processing
Software
Name
Version
Classification
PHENIX
1.7.3_928
refinement
XSCALE
datascaling
PDB_EXTRACT
3.27
dataextraction
XDS
datareduction
PHENIX
phasing
Refinement
Method to determine structure: AB INITIO PHASING / Resolution: 2.2→47.193 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.18 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Rfree
0.2807
473
4.81 %
Rwork
0.2293
9368
-
obs
0.2316
9841
99.95 %
Solvent computation
Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.085 Å2 / ksol: 0.331 e/Å3
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