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- EMDB-28019: Tail tube of P1 bacteriophage -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-28019
TitleTail tube of P1 bacteriophage
Map dataTail Tube of P1 bacteriophage
Sample
  • Virus: Escherichia phage P1 (virus)
Keywordsphage tail / helical / cryo-TEM / CONTRACTILE PROTEIN / STRUCTURAL PROTEIN
Function / homologyBplB
Function and homology information
Biological speciesEscherichia phage P1 (virus)
Methodhelical reconstruction / cryo EM / Resolution: 3.23 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 tube of P1 bacteriophage
Authors: Sen A / Bhatt V / Kim K / Bouchet-Marquis C
History
DepositionSep 2, 2022-
Header (metadata) releaseOct 5, 2022-
Map releaseOct 5, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28019.png

Downloads & links

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Map

FileDownload / File: emd_28019.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTail Tube of P1 bacteriophage
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.69 Å/pix.
x 512 pix.
= 355.558 Å		0.69 Å/pix.
x 512 pix.
= 355.558 Å		0.69 Å/pix.
x 512 pix.
= 355.558 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.69445 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.2511862 - 0.44138345
Average (Standard dev.)0.0039807186 (±0.017768841)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-256-256-256
Dimensions512512512
Spacing512512512
CellA=B=C: 355.5584 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: A half Map of Tail tube of Bacteriophage P1

Fileemd_28019_half_map_1.map
AnnotationA _half Map of Tail tube of Bacteriophage P1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: B half Map of Tail tube of Bacteriophage P1

Fileemd_28019_half_map_2.map
AnnotationB _half Map of Tail tube of Bacteriophage P1
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

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical 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

Final reconstructionApplied symmetry - Helical parameters - Δz: 39.15 Å
Applied symmetry - Helical parameters - Δ&Phi: 19.32 °
Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 98652
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE

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