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- EMDB-63704: Tomogram of bacteriophage NF5-infected Brochothrix thermosphacta ... -

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Basic information

Entry
Database: EMDB / ID: EMD-63704
TitleTomogram of bacteriophage NF5-infected Brochothrix thermosphacta cell (1 out of 2)
Map data
Sample
  • Cell: Bacteriophage NF5-infected Brochothrix thermosphacta cell
Keywordsphage / Brochothrix thermosphacta / viral infection / Gram-positive bacteria / VIRUS
Biological speciesBrochothrix phage NF5 (virus)
Methodelectron tomography / cryo EM
AuthorsPeng YN / Liu HR
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)32071209 China
CitationJournal: To Be Published
Title: structure of bacteriophage NF5
Authors: Peng YN / Liu HR
History
DepositionMar 11, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63704.png

Downloads & links

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Map

FileDownload / File: emd_63704.map.gz / Format: CCP4 / Size: 800 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.18 Å/pix.
x 400 pix.
= 1272. Å		3.18 Å/pix.
x 1024 pix.
= 3256.32 Å		3.18 Å/pix.
x 1024 pix.
= 3256.32 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 3.18 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-32768.0 - 32767.0
Average (Standard dev.)12806.113999999999578 (±2503.338600000000042)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions10241024400
Spacing10241024400
CellA: 3256.32 Å / B: 3256.32 Å / C: 1272.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Bacteriophage NF5-infected Brochothrix thermosphacta cell

EntireName: Bacteriophage NF5-infected Brochothrix thermosphacta cell
Components
  • Cell: Bacteriophage NF5-infected Brochothrix thermosphacta cell

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Supramolecule #1: Bacteriophage NF5-infected Brochothrix thermosphacta cell

SupramoleculeName: Bacteriophage NF5-infected Brochothrix thermosphacta cell
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Brochothrix phage NF5 (virus)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 1 / Focused ion beam - Duration: 10 / Focused ion beam - Temperature: 100 K / Focused ion beam - Initial thickness: 1000 / Focused ion beam - Final thickness: 250
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is TFS Aquilos 2. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm

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Image processing

Final reconstructionNumber images used: 36
CTF correctionType: NONE

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