Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97625 Å / Relative weight: 1
Reflection
Resolution: 1.39→39.03 Å / Num. obs: 26727 / % possible obs: 98.5 % / Redundancy: 4.1 % / Rpim(I) all: 0.043 / Rrim(I) all: 0.094 / Rsym value: 0.083 / Net I/av σ(I): 3.5 / Net I/σ(I): 9
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
1.39-1.47
2.9
0.513
1.5
10608
3684
0.338
0.619
0.513
1.9
95.2
1.47-1.55
4
0.37
2
14405
3645
0.206
0.426
0.37
3.3
98.7
1.55-1.66
4
0.271
2.6
13656
3438
0.15
0.312
0.271
4.4
98.7
1.66-1.79
4.4
0.186
3.7
14135
3221
0.1
0.212
0.186
6.4
99.1
1.79-1.97
4.2
0.129
5
12381
2951
0.071
0.148
0.129
8.6
98.9
1.97-2.2
4.5
0.095
5.6
12302
2708
0.05
0.108
0.095
12.7
99.1
2.2-2.54
4.5
0.086
6.4
10949
2425
0.045
0.097
0.086
15
99.3
2.54-3.11
4.8
0.077
6.6
10027
2068
0.039
0.086
0.077
18.1
99.7
3.11-4.4
4.6
0.069
6.5
7530
1627
0.036
0.078
0.069
19.8
99.4
4.4-39.025
4.5
0.063
7.7
4345
960
0.031
0.07
0.063
20
99.1
-
Processing
Software
Name
Version
Classification
XDS
datareduction
SCALA
3.3.20
datascaling
REFMAC
5.8.0257
refinement
PDB_EXTRACT
3.25
dataextraction
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: In house structure Resolution: 1.39→39.03 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.299 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.068 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2037
1348
5 %
RANDOM
Rwork
0.1717
-
-
-
obs
0.1732
25379
98.17 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
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