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- EMDB-37189: Three-fold Melbournevirus block (PASR pre-processed K2 counting m... -

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Basic information

Entry
Database: EMDB / ID: EMD-37189
TitleThree-fold Melbournevirus block (PASR pre-processed K2 counting mode data)
Map dataPost-processed map 3F Melbournevirus block (PASR pre-processed K2 counting mode data)
Sample
  • Virus: Melbournevirus
KeywordsPASR / post-acquisition super resolution / Melbournevirus / block-based reconstruction / VIRUS
Biological speciesMelbournevirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.48 Å
AuthorsBurton-Smith RN / Murata K
Funding support Japan, 1 items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
CitationJournal: To Be Published
Title: Three-fold Melbournevirus block (PASR pre-processed K2 counting mode data)
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_37189.png

Downloads & links

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Map

FileDownload / File: emd_37189.map.gz / Format: CCP4 / Size: 2.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost-processed map 3F Melbournevirus block (PASR pre-processed K2 counting mode data)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 900 pix.
= 994.5 Å		1.11 Å/pix.
x 900 pix.
= 994.5 Å		1.11 Å/pix.
x 900 pix.
= 994.5 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: 0.017
Minimum - Maximum-0.055623025 - 0.09152288
Average (Standard dev.)0.00033585154 (±0.0044319574)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions900900900
Spacing900900900
CellA=B=C: 994.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half-map 1 3F Melbournevirus block (PASR pre-processed K2...

Fileemd_37189_half_map_1.map
AnnotationHalf-map 1 3F Melbournevirus block (PASR pre-processed K2 counting mode data)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2 3F Melbournevirus block (PASR pre-processed K2...

Fileemd_37189_half_map_2.map
AnnotationHalf-map 2 3F Melbournevirus block (PASR pre-processed K2 counting mode data)
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: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 235140
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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