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- EMDB-42104: The second conformation of gp1-gp4-gp5 from bacteriophage P22 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-42104
TitleThe second conformation of gp1-gp4-gp5 from bacteriophage P22
Map data
Sample
  • Virus: Salmonella phage P22 (virus)
KeywordsBacteriophage P22 / capsid-portal / VIRAL PROTEIN
Biological speciesSalmonella phage P22 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsWang C / Liu J / Molineux IJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Structural insights into bacteriophage P22 assembly and infection initiation.
Authors: Wang C / Liu J / Molineux IJ
History
DepositionSep 25, 2023-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateOct 2, 2024-
Current statusOct 2, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42104.png

Downloads & links

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Map

FileDownload / File: emd_42104.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 480 pix.
= 512.64 Å		1.07 Å/pix.
x 480 pix.
= 512.64 Å		1.07 Å/pix.
x 480 pix.
= 512.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.068 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009
Minimum - Maximum-0.0072522564 - 1.9107155
Average (Standard dev.)0.0027430747 (±0.041613314)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 512.63995 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_42104_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_42104_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Salmonella phage P22

EntireName: Salmonella phage P22 (virus)
Components
  • Virus: Salmonella phage P22 (virus)

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Supramolecule #1: Salmonella phage P22

SupramoleculeName: Salmonella phage P22 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 2908168 / Sci species name: Salmonella phage P22 / Virus type: VIRION / Virus isolate: STRAIN / 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: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 43763
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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