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- EMDB-66427: Melbournevirus fivefold block (CryoSPARC processed with PASR) -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-66427
TitleMelbournevirus fivefold block (CryoSPARC processed with PASR)
Map dataMelbV 5F CryoSPARC PASR sharpened map
Sample
  • Virus: Marseillevirus sp. 'Melbournevirus'
KeywordsGiant virus / NCLDV / PASR / VIRUS
Biological speciesMarseillevirus sp. 'Melbournevirus'
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsBurton-Smith RN
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To be published
Title: Post-acquisition super resolution for cryo-electron microscopy
Authors: Burton-Smith RN / Murata K
History
DepositionSep 30, 2025-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_66427.png

Downloads & links

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Map

FileDownload / File: emd_66427.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMelbV 5F CryoSPARC PASR sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 768 pix.
= 848.64 Å		1.11 Å/pix.
x 768 pix.
= 848.64 Å		1.11 Å/pix.
x 768 pix.
= 848.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.105 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.105
Minimum - Maximum-0.42368594 - 0.66070247
Average (Standard dev.)-0.000012207538 (±0.03484831)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions768768768
Spacing768768768
CellA=B=C: 848.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: MelbV 5F CryoSPARC PASR unsharpened map

Fileemd_66427_additional_1.map
AnnotationMelbV 5F CryoSPARC PASR unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: MelbV 5F CryoSPARC PASR half map 2

Fileemd_66427_half_map_1.map
AnnotationMelbV 5F CryoSPARC PASR half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: MelbV 5F CryoSPARC PASR half map 1

Fileemd_66427_half_map_2.map
AnnotationMelbV 5F CryoSPARC PASR half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Marseillevirus sp. 'Melbournevirus'

EntireName: Marseillevirus sp. 'Melbournevirus'
Components
  • Virus: Marseillevirus sp. 'Melbournevirus'

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Supramolecule #1: Marseillevirus sp. 'Melbournevirus'

SupramoleculeName: Marseillevirus sp. 'Melbournevirus' / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 1560514 / Sci species name: Marseillevirus sp. 'Melbournevirus' / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 73143
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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