Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O
-
Details
Sequence details
RESIDUE 90-134 ARE FROM HUMICOLA INSOLENS CEL6A. RESIDUE 135-308 AND 401-447 ARE FROM HYPOCREA ...RESIDUE 90-134 ARE FROM HUMICOLA INSOLENS CEL6A. RESIDUE 135-308 AND 401-447 ARE FROM HYPOCREA JECORINA CEL6A. RESIDUE 309-400 ARE FROM CHAETOMIUM THERMOPHILUM CEL6A.
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.63 Å3/Da / Density % sol: 53.3 %
Crystal grow
Method: vapor diffusion, sitting drop / pH: 5.75 / Details: pH 5.75, VAPOR DIFFUSION, SITTING DROP
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.033 Å / Relative weight: 1
Reflection
Resolution: 1.5→35.309 Å / Num. all: 65106 / Num. obs: 65106 / % possible obs: 97.9 % / Redundancy: 3.4 % / Rsym value: 0.041 / Net I/σ(I): 16.1
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
1.5-1.58
3.2
0.365
2.1
30476
9401
0.365
97.7
1.58-1.68
3.5
0.237
3.3
31323
9047
0.237
98.7
1.68-1.79
3.5
0.157
4.9
29060
8421
0.157
98.1
1.79-1.94
3.2
0.093
8.2
25231
7777
0.093
97.4
1.94-2.12
3.6
0.06
12.4
25852
7279
0.06
98.8
2.12-2.37
3.5
0.043
16.4
23014
6598
0.043
98.2
2.37-2.74
3.2
0.036
18.9
18318
5670
0.036
96.4
2.74-3.35
3.5
0.029
20.8
17440
4962
0.029
98.8
3.35-4.74
3.4
0.025
23.8
12852
3807
0.025
97.3
4.74-35.309
3.3
0.027
21.7
7018
2144
0.027
97.1
-
Processing
Software
Name
Version
Classification
NB
SCALA
3.3.16
datascaling
REFMAC
refinement
PDB_EXTRACT
3.11
dataextraction
MOLREP
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→35.309 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.1802 / WRfactor Rwork: 0.154 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9025 / SU B: 2.055 / SU ML: 0.039 / SU R Cruickshank DPI: 0.0603 / SU Rfree: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1808
3260
5 %
RANDOM
Rwork
0.1543
-
-
-
obs
0.1557
65102
97.7 %
-
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