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- EMDB-3655: Cryo-Electron Microscopy Structure of the Macrobrachium rosenberg... -

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Entry
Database: EMDB / ID: 3655
TitleCryo-Electron Microscopy Structure of the Macrobrachium rosenbergii Nodavirus Capsid at 7 Angstroms Resolution
Map dataMacrobrachium rosenbergii nodavirus virus-like particle.
SampleMacrobrachium rosenbergii Nodavirus Capsid:
virus
SourceMacrobrachium rosenbergii Nodavirus
Methodsingle particle reconstruction / cryo EM / 7.5 Å resolution
AuthorsBhella D / Ho KL
CitationJournal: Sci Rep / Year: 2017
Title: Cryo-Electron Microscopy Structure of the Macrobrachium rosenbergii Nodavirus Capsid at 7 Angstroms Resolution.
Authors: Kok Lian Ho / Chare Li Kueh / Poay Ling Beh / Wen Siang Tan / David Bhella
DateDeposition: Mar 29, 2017 / Header (metadata) release: Apr 5, 2017 / Map release: May 31, 2017 / Last update: Jul 12, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3655.map.gz (map file in CCP4 format, 536871 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
512 pix
1.09 Å/pix.
= 558.08 Å
512 pix
1.09 Å/pix.
= 558.08 Å
512 pix
1.09 Å/pix.
= 558.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density
Contour Level:0.04 (by author), 0.04 (movie #1):
Minimum - Maximum-0.14659674 - 0.20144895
Average (Standard dev.)0.0033128622 (0.014665142)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions512512512
Origin0.00.00.0
Limit511.0511.0511.0
Spacing512512512
CellA=B=C: 558.08 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z558.080558.080558.080
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.1470.2010.003

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Supplemental data

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Sample components

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Entire Macrobrachium rosenbergii Nodavirus Capsid

EntireName: Macrobrachium rosenbergii Nodavirus Capsid / Number of components: 1

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Component #1: virus, Macrobrachium rosenbergii Nodavirus

VirusName: Macrobrachium rosenbergii Nodavirus / Class: VIRUS-LIKE PARTICLE / Empty: No / Enveloped: No / Isolate: OTHER
SpeciesSpecies: Macrobrachium rosenbergii Nodavirus
Source (natural)Host Species: Macrobrachium rosenbergii

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.2
Support filmC-flats had an additional carbon evaporation applied
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 % / Details: Blot for 4 seconds, Blot force 25.

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Electron microscopy imaging

ImagingMicroscope: JEOL 2200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 7 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: DIRECT ELECTRON DE-20 (5k x 3k)

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Image acquisition

Image acquisitionNumber of digital images: 281

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 1658
3D reconstructionAlgorithm: BACK PROJECTION / Software: RELION / Resolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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