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- EMDB-46705: Subtomogram averaging of Bxb1 phage tail tube (emptied) during th... -

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Basic information

Entry
Database: EMDB / ID: EMD-46705
TitleSubtomogram averaging of Bxb1 phage tail tube (emptied) during the infection state
Map dataSubtomogram averaging of Bxb1 phage tail tube (emptied) during the infection state
Sample
  • Virus: Bxb1 (virus)
KeywordsPhage / tuberculosis / mycobacterium / VIRUS
Biological speciesBxb1 (virus)
Methodsubtomogram averaging / cryo EM / Resolution: 22.0 Å
AuthorsPark D / Mondal S
Funding support United States, 1 items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: Structure and infection dynamics of mycobacteriophage Bxb1
Authors: Freeman KG / Mondal S / Macale LS / Podgorski J / White SJ / Silva BH / Ortiz V / Huet A / Narsico JT / Ho M / Jacobs-Sera D / Lowary TL / Conway JF / Park D / hatfull GH
History
DepositionAug 23, 2024-
Header (metadata) releaseSep 18, 2024-
Map releaseSep 18, 2024-
UpdateSep 18, 2024-
Current statusSep 18, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46705.png

Downloads & links

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Map

FileDownload / File: emd_46705.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram averaging of Bxb1 phage tail tube (emptied) during the infection state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.66 Å/pix.
x 180 pix.
= 299.34 Å		1.66 Å/pix.
x 180 pix.
= 299.34 Å		1.66 Å/pix.
x 180 pix.
= 299.34 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.663 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1907.0
Minimum - Maximum0.0 - 4094.0
Average (Standard dev.)1785.574599999999919 (±272.258899999999983)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 299.34 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_46705_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_46705_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 : Bxb1

EntireName: Bxb1 (virus)
Components
  • Virus: Bxb1 (virus)

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Supramolecule #1: Bxb1

SupramoleculeName: Bxb1 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 2902907 / Sci species name: Bxb1 / 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
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 4.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 (ver. 99.58) / Number subtomograms used: 214
ExtractionNumber tomograms: 282 / Number images used: 214 / Software - Name: EMAN2 (ver. 2.99)
Final angle assignmentType: OTHER / Software - Name: EMAN2 (ver. 99.58)
FSC plot (resolution estimation)

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