Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
Detector
Type: ADSC QUANTUM 315r / Detector: CCD
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1 Å / Relative weight: 1
Reflection
Resolution: 2→50 Å / Num. obs: 26396 / % possible obs: 98.2 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.038 / Χ2: 0.81 / Net I/σ(I): 13.9
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Num. unique all
Χ2
Diffraction-ID
% possible all
2-2.03
2.4
0.156
1132
0.611
1
88
2.03-2.07
2.8
0.153
1226
0.794
1
92.4
2.07-2.11
2.9
0.133
1234
0.821
1
94.8
2.11-2.15
3.1
0.114
1293
0.796
1
96.1
2.15-2.2
3.2
0.105
1277
0.804
1
96.7
2.2-2.25
3.4
0.109
1305
1.025
1
98.6
2.25-2.31
3.7
0.103
1321
0.954
1
100
2.31-2.37
3.7
0.087
1327
0.854
1
99.8
2.37-2.44
3.7
0.076
1348
0.794
1
99.9
2.44-2.52
3.7
0.065
1303
0.787
1
99.9
2.52-2.61
3.7
0.06
1331
0.766
1
100
2.61-2.71
3.6
0.052
1337
0.778
1
100
2.71-2.84
3.7
0.045
1345
0.8
1
100
2.84-2.99
3.7
0.04
1351
0.789
1
100
2.99-3.17
3.7
0.034
1347
0.787
1
100
3.17-3.42
3.6
0.028
1343
0.772
1
100
3.42-3.76
3.6
0.026
1368
0.893
1
100
3.76-4.31
3.6
0.023
1376
0.739
1
100
4.31-5.43
3.5
0.023
1387
0.73
1
100
5.43-50
3.4
0.024
1445
0.816
1
97
-
Processing
Software
Name
Version
Classification
NB
SCALEPACK
datascaling
REFMAC
5.6.0117
refinement
PDB_EXTRACT
3.14
dataextraction
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→36.13 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.504 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2214
1323
5 %
RANDOM
Rwork
0.1747
-
-
-
obs
0.177
26311
98.26 %
-
all
-
26396
-
-
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