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- EMDB-49262: C3 baseplate consensus reconstruction of JohannRWettstein (Bas63) -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-49262
TitleC3 baseplate consensus reconstruction of JohannRWettstein (Bas63)
Map dataC3 baseplate consensus reconstruction of JohannRWettstein (Bas63)
Sample
  • Virus: Escherichia phage JohannRWettstein (virus)
Keywordsbaseplate / wedge / hub / phage / bacteriophage / VIRAL PROTEIN
Biological speciesEscherichia phage JohannRWettstein (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.83 Å
AuthorsHodgkinson-Bean J
Funding support Japan, 2 items
OrganizationGrant numberCountry
Ministry of Agriculture, Forestry and Fisheries (MAFF)GD0696J004 Japan
Japan Society for the Promotion of Science (JSPS)21K20645 Japan
CitationJournal: To Be Published
Title: Icosahedral capsid assembly of phage JohannRWettstein (Bas63)
Authors: Hodgkinson-Bean J / Ayala R / McJarrow-Keller K / Cassin L / Rutter GL / Crowe AJM / Wolf M / Bostina M
History
DepositionFeb 17, 2025-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49262.png

Downloads & links

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Map

FileDownload / File: emd_49262.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationC3 baseplate consensus reconstruction of JohannRWettstein (Bas63)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 400 pix.
= 554.8 Å		1.39 Å/pix.
x 400 pix.
= 554.8 Å		1.39 Å/pix.
x 400 pix.
= 554.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.387 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.719
Minimum - Maximum-1.3620628 - 2.5095499
Average (Standard dev.)-0.0015540998 (±0.15162168)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 554.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_49262_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_49262_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Escherichia phage JohannRWettstein

EntireName: Escherichia phage JohannRWettstein (virus)
Components
  • Virus: Escherichia phage JohannRWettstein (virus)

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Supramolecule #1: Escherichia phage JohannRWettstein

SupramoleculeName: Escherichia phage JohannRWettstein / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 / NCBI-ID: 2852035 / Sci species name: Escherichia phage JohannRWettstein / Virus type: VIRION / Virus isolate: SPECIES / 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-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 49.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 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: 3.83 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 14390
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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