|Entry||Database: EMDB / ID: 9040|
|Title||Analysis of bacteriophage phiX174 tomograms using the locked self-rotation function|
|Map data||The map was calculated by averaging of ten icosahedrally-averaged maps of individual phiX174 particles.|
|Sample||Enterobacteria phage phiX174:|
|Source||Enterobacteria phage phiX174 (virus)|
|Method||electron tomography / cryo EM|
|Authors||Fokine A / Sun Y / Khare B / Rossmann MG|
|Citation||Journal: J. Struct. Biol. / Year: 2019|
Title: Enhancement of tomogram interpretability using the locked self-rotation function.
Authors: Andrei Fokine / Baldeep Khare / Yingyuan Sun / Michael G Rossmann
Abstract: The interpretation of cryo-electron tomograms of macromolecular complexes can be difficult because of the large amount of noise and because of the missing wedge effect. Here it is shown how the ...The interpretation of cryo-electron tomograms of macromolecular complexes can be difficult because of the large amount of noise and because of the missing wedge effect. Here it is shown how the presence of rotational symmetry in a sample can be utilized to enhance the quality of a tomographic analysis. The orientation of symmetry axes in a sub-tomogram can be determined using a locked self-rotation function. Given this knowledge, the sub-tomogram density can then be averaged to improve its interpretability. Sub-tomograms of the icosahedral bacteriophage phiX174 are used to demonstrate the procedure.
|Date||Deposition: Aug 13, 2018 / Header (metadata) release: Sep 19, 2018 / Map release: Feb 27, 2019 / Last update: Mar 27, 2019|
|Structure viewer||EM map: |
Downloads & links
|File||emd_9040.map.gz (map file in CCP4 format, 2049 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 5.2 Å|
CCP4 map header:
-Entire Enterobacteria phage phiX174
|Entire||Name: Enterobacteria phage phiX174 / Details: The virus was grown in E.coli cells. / Number of components: 1|
-Component #1: virus, Enterobacteria phage phiX174
|Virus||Name: Enterobacteria phage phiX174 / Class: VIRION / Details: The virus was grown in E.coli cells. / Empty: No / Enveloped: No / Isolate: STRAIN|
|Species||Species: Enterobacteria phage phiX174 (virus)|
|Source (natural)||Host Species: Escherichia coli (E. coli)|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||pH: 7.4|
|Vitrification||Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.73 e/Å2 / Illumination mode: OTHER|
|Lens||Magnification: 11000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 3000.0 - nm|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Processing||Method: electron tomography / Number of sections: 41|
|3D reconstruction||Algorithm: BACK PROJECTION / Software: IMOD|
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