Mass: 55910.215 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nonlabens dokdonensis DSW-6 (bacteria) / Gene: DDD_2394 / Production host: Escherichia coli (E. coli) References: UniProt: L7WC64, Oxidoreductases; Acting on the CH-CH group of donors; With unknown physiological acceptors
Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 2
-
Sample preparation
Crystal
Density Matthews: 2.01 Å3/Da / Density % sol: 38.91 %
Crystal grow
Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 14% PEG3350, 0.1 M succinic acid, pH 7.0, 50 mM dimethylbenzylammonium propane sulfonate, VAPOR DIFFUSION, HANGING DROP, temperature 295K
-
Data collection
Diffraction
ID
Mean temperature (K)
Crystal-ID
1
100
1
2
100
1
Diffraction source
Source
Site
Beamline
ID
Wavelength (Å)
SYNCHROTRON
PAL/PLS
7A (6B, 6C1)
1
1
SYNCHROTRON
SPring-8
BL26B1
2
0.97939
Detector
Type
ID
Detector
Date
ADSC QUANTUM 270r
1
CCD
Dec 14, 2011
RIGAKU JUPITER 210
2
CCD
Mar 21, 2012
Radiation
ID
Monochromator
Protocol
Monochromatic (M) / Laue (L)
Scattering type
Wavelength-ID
1
doublecrystalSi(111)
SINGLEWAVELENGTH
M
x-ray
1
2
doublecrystalSi(111)
SINGLEWAVELENGTH
M
x-ray
1
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
1
1
2
0.97939
1
Reflection
Resolution: 1.97→50 Å / Num. obs: 30536 / % possible obs: 97.1 % / Redundancy: 3 % / Rmerge(I) obs: 0.067 / Χ2: 1.368 / Net I/σ(I): 11.4
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Num. unique all
Χ2
Diffraction-ID
% possible all
1.97-2
2.1
0.268
1325
0.826
1,2
83.8
2-2.04
2.2
0.237
1411
0.836
1,2
91
2.04-2.08
2.4
0.222
1491
0.878
1,2
93.1
2.08-2.12
2.5
0.222
1474
0.949
1,2
96
2.12-2.17
2.5
0.21
1489
0.87
1,2
96.2
2.17-2.22
2.7
0.195
1534
0.954
1,2
97.4
2.22-2.27
2.7
0.183
1530
1.008
1,2
97.5
2.27-2.34
2.8
0.172
1512
1.144
1,2
98
2.34-2.4
2.9
0.143
1523
1.063
1,2
98
2.4-2.48
2.9
0.134
1537
1.069
1,2
98
2.48-2.57
2.9
0.119
1575
1.157
1,2
98.4
2.57-2.67
3
0.111
1534
1.148
1,2
99.3
2.67-2.8
3.1
0.096
1537
1.212
1,2
99
2.8-2.94
3.2
0.087
1582
1.261
1,2
98.9
2.94-3.13
3.3
0.069
1550
1.288
1,2
99.4
3.13-3.37
3.4
0.06
1567
1.509
1,2
99.6
3.37-3.71
3.5
0.061
1573
2.215
1,2
99.7
3.71-4.24
3.6
0.055
1573
2.667
1,2
99.9
4.24-5.35
3.7
0.038
1593
1.745
1,2
99.7
5.35-50
3.6
0.032
1626
1.531
1,2
99.7
-
Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
REFMAC
5.7.0032
refinement
PDB_EXTRACT
3.15
dataextraction
HKL-2000
datacollection
HKL-2000
datareduction
SOLVE
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.97→48.08 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.547 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.192 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2235
1535
5 %
RANDOM
Rwork
0.1602
-
-
-
obs
0.1634
28990
96.94 %
-
all
-
30525
-
-
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