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- EMDB-67125: The overall tail of phage PhiKZ -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-67125
TitleThe overall tail of phage PhiKZ
Map data
Sample
  • Virus: Pseudomonas phage phiKZ (virus)
Keywordsoverall tail / VIRUS
Biological speciesPseudomonas phage phiKZ (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.61 Å
AuthorsXiao H / Peng Z / Zhou J / Liu H
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)32430020 China
National Natural Science Foundation of China (NSFC)32200994 China
CitationJournal: To Be Published
Title: Structural atlas of the intact jumbo phage phiKZ
Authors: Xiao H / Peng Z / Zhou J / Liu H
History
DepositionNov 18, 2025-
Header (metadata) releaseFeb 11, 2026-
Map releaseFeb 11, 2026-
UpdateFeb 11, 2026-
Current statusFeb 11, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_67125.png

Downloads & links

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Map

FileDownload / File: emd_67125.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.06 Å/pix.
x 800 pix.
= 2448. Å		3.06 Å/pix.
x 800 pix.
= 2448. Å		3.06 Å/pix.
x 800 pix.
= 2448. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-1.5775663 - 2.8739896
Average (Standard dev.)0.00014095192 (±0.1230976)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 2448.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_67125_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_67125_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_67125_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 : Pseudomonas phage phiKZ

EntireName: Pseudomonas phage phiKZ (virus)
Components
  • Virus: Pseudomonas phage phiKZ (virus)

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Supramolecule #1: Pseudomonas phage phiKZ

SupramoleculeName: Pseudomonas phage phiKZ / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 / NCBI-ID: 2905945 / Sci species name: Pseudomonas phage phiKZ / 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

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.61 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 8843
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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