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- EMDB-70328: Pseudomonas phage PP7 icosahedral T3 cage -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-70328
TitlePseudomonas phage PP7 icosahedral T3 cage
Map datasharpened map
Sample
  • Complex: Pseudomonas phage PP7 icosahedral T3 cage
KeywordsIn comparison to 4D-STEM / VIRUS LIKE PARTICLE
Biological speciesPseudomonas phage PP7 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsYu Y / Kopylov M
Funding support United States, 1 items
OrganizationGrant numberCountry
Chan Zuckerberg Initiative United States
CitationJournal: To Be Published
Title: Pseudomonas phage PP7 icosahedral T3 cage
Authors: Yu Y / Kopylov M
History
DepositionApr 25, 2025-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateMay 7, 2025-
Current statusMay 7, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70328.png

Downloads & links

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Map

FileDownload / File: emd_70328.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 400 pix.
= 430.4 Å		1.08 Å/pix.
x 400 pix.
= 430.4 Å		1.08 Å/pix.
x 400 pix.
= 430.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.076 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.528
Minimum - Maximum-0.7416664 - 1.7440344
Average (Standard dev.)0.009193734 (±0.111078665)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 430.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70328_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: un-sharpened map

Fileemd_70328_additional_1.map
Annotationun-sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_70328_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_70328_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 : Pseudomonas phage PP7 icosahedral T3 cage

EntireName: Pseudomonas phage PP7 icosahedral T3 cage
Components
  • Complex: Pseudomonas phage PP7 icosahedral T3 cage

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Supramolecule #1: Pseudomonas phage PP7 icosahedral T3 cage

SupramoleculeName: Pseudomonas phage PP7 icosahedral T3 cage / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Pseudomonas phage PP7 (virus)
Molecular weightTheoretical: 7.5 MDa

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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

Concentration1 mg/mL
BufferpH: 7 / Details: 100 mM potassium phosphage buffer
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsSpherical aberration corrector: Cs corrected
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.18 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 1.8 µm / Calibrated defocus min: 1.1 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.0001 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
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: INSILICO MODEL / In silico model: Cryosparc ab initio model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 900
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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