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- EMDB-37169: Melbournevirus (whole virus, Bayesian polished reconstruction, re... -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-37169
TitleMelbournevirus (whole virus, Bayesian polished reconstruction, realigned to I1 symmetry)
Map dataPost-processed polished MelbV WHOLEMAP
Sample
  • Virus: Melbournevirus
KeywordsMelbournevirus / giant virus / NCLDV / VIRUS
Biological speciesMelbournevirus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.42 Å
AuthorsBurton-Smith RN / Murata K
Funding support Japan, Sweden, 4 items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP19H04845 Japan
Swedish Research Council2018-03387 Sweden
The Swedish Foundation for Strategic ResearchJA2014-5721 Sweden
Swedish Research Council2018-00421 Sweden
CitationJournal: To Be Published
Title: Melbournevirus (whole virus, Bayesian polished reconstruction, realigned to I1 symmetry)
Authors: Burton-Smith RN / Murata K
History
DepositionAug 13, 2023-
Header (metadata) releaseJan 17, 2024-
Map releaseJan 17, 2024-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37169.png

Downloads & links

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Map

FileDownload / File: emd_37169.map.gz / Format: CCP4 / Size: 11.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost-processed polished MelbV WHOLEMAP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.21 Å/pix.
x 1440 pix.
= 3182.4 Å		2.21 Å/pix.
x 1440 pix.
= 3182.4 Å		2.21 Å/pix.
x 1440 pix.
= 3182.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.21 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.016
Minimum - Maximum-0.03234062 - 0.06504781
Average (Standard dev.)-0.00008390786 (±0.0050965645)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions144014401440
Spacing144014401440
CellA=B=C: 3182.4001 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Post-processed masked polished MelbV WHOLEMAP

Fileemd_37169_additional_1.map
AnnotationPost-processed masked polished MelbV WHOLEMAP
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 1 polished MelbV WHOLEMAP

Fileemd_37169_half_map_1.map
AnnotationHalf-map 1 polished MelbV WHOLEMAP
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2 polished MelbV WHOLEMAP

Fileemd_37169_half_map_2.map
AnnotationHalf-map 2 polished MelbV WHOLEMAP
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Melbournevirus

EntireName: Melbournevirus
Components
  • Virus: Melbournevirus

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Supramolecule #1: Melbournevirus

SupramoleculeName: Melbournevirus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 1560514 / Sci species name: 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 26.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.42 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 3124
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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