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- EMDB-8916: Single-particle reconstruction of reovirus T1L -

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Open data


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Basic information

Entry
Database: EMDB / ID: 8916
TitleSingle-particle reconstruction of reovirus T1L
Map dataSurface rendering of Reovirus T1L
SampleReovirusReoviridae:
virus
SourceReovirus sp.
Methodsingle particle reconstruction / cryo EM / 8.2 Å resolution
AuthorsSnyder AJ / Wang JCY / Danthi P
CitationJournal: To be Published
Title: The reovirus mu1 protein contributes to the environmental stability of virions
Authors: Snyder AJ / Wang JCY / Danthi P
DateDeposition: Jun 25, 2018 / Header (metadata) release: Jul 4, 2018 / Map release: Jul 4, 2018 / Last update: Jul 4, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.005
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.005
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8916.map.gz (map file in CCP4 format, 256001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
400 pix
2.5 Å/pix.
= 1000. Å
400 pix
2.5 Å/pix.
= 1000. Å
400 pix
2.5 Å/pix.
= 1000. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.5 Å
Density
Contour Level:0.005 (by author), 0.005 (movie #1):
Minimum - Maximum-0.019065678 - 0.021191198
Average (Standard dev.)0.0002982313 (0.0031632492)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions400400400
Origin0.0.0.
Limit399.399.399.
Spacing400400400
CellA=B=C: 1000.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.52.52.5
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z1000.0001000.0001000.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0190.0210.000

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Supplemental data

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Sample components

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Entire Reovirus

EntireName: Reovirus / Number of components: 1

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Component #1: virus, Reovirus sp.

VirusName: Reovirus sp. / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Reovirus sp.
Source (engineered)Expression System: Mus musculus (house mouse)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

ImagingMicroscope: JEOL 3200FS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: DIRECT ELECTRON DE-20 (5k x 3k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 10568
3D reconstructionResolution: 8.2 Å / Resolution method: FSC 0.143 CUT-OFF

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