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- EMDB-27716: Capsid of P1 bacteriophage -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-27716
TitleCapsid of P1 bacteriophage
Map dataCapsid of P1 bacteriophage
Sample
  • Virus: Escherichia phage P1 (virus)
Keywordscapsid protein of P1 bacteriophage / VIRUS
Biological speciesEscherichia phage P1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsSen A / Bhatt V / Kim K / Bouchet-Marquis C
Funding support United States, 1 items
OrganizationGrant numberCountry
Other government United States
CitationJournal: To Be Published
Title: Tail of P1 bacteriophage
Authors: Sen A / Bouchet-Marquis C / Kim K / Bhatt V
History
DepositionJul 27, 2022-
Header (metadata) releaseAug 30, 2023-
Map releaseAug 30, 2023-
UpdateAug 30, 2023-
Current statusAug 30, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27716.png

Downloads & links

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Map

FileDownload / File: emd_27716.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCapsid of P1 bacteriophage
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 800 pix.
= 1111.12 Å		1.39 Å/pix.
x 800 pix.
= 1111.12 Å		1.39 Å/pix.
x 800 pix.
= 1111.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3889 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.16066 - 0.29955438
Average (Standard dev.)0.0061403536 (±0.03922401)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-400-400-400
Dimensions800800800
Spacing800800800
CellA=B=C: 1111.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_27716_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map of Capsid of P1 bacteriophage

Fileemd_27716_half_map_1.map
Annotationhalf map of Capsid of P1 bacteriophage
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map of Capsid of P1 bacteriophage

Fileemd_27716_half_map_2.map
Annotationhalf map of Capsid of P1 bacteriophage
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 P1

EntireName: Escherichia phage P1 (virus)
Components
  • Virus: Escherichia phage P1 (virus)

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Supramolecule #1: Escherichia phage P1

SupramoleculeName: Escherichia phage P1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 2886926 / Sci species name: Escherichia phage P1 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Virus shellShell ID: 1 / Name: capsid / Diameter: 1020.0 Å

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average exposure time: 9.4 sec. / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 73000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 60742
Initial angle assignmentType: NOT APPLICABLE / Software - Name: Bsoft
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC

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