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- EMDB-28761: Mycobacterium phage Che8 mutant capsid (gene 110 deletion) -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-28761
TitleMycobacterium phage Che8 mutant capsid (gene 110 deletion)
Map dataSharpened map of Che_mutant_map.mrc.
Sample
  • Virus: Mycobacterium phage Che8 (virus)
KeywordsHK97-fold / T=9 / tailed bacteriophage / VIRUS
Biological speciesMycobacterium phage Che8 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.39 Å
AuthorsPodgorski JM / White SJ
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Diverse O-linked Glycosylation of phage structural proteins is mediated through phage-encoded glycosyltransferases.
Authors: Pope WH / Hatfull GF
History
DepositionNov 3, 2022-
Header (metadata) releaseNov 8, 2023-
Map releaseNov 8, 2023-
UpdateNov 8, 2023-
Current statusNov 8, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28761.png

Downloads & links

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Map

FileDownload / File: emd_28761.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of Che_mutant_map.mrc.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.18 Å/pix.
x 800 pix.
= 945.6 Å		1.18 Å/pix.
x 800 pix.
= 945.6 Å		1.18 Å/pix.
x 800 pix.
= 945.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.182 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.5
Minimum - Maximum-8.98274 - 23.532883000000002
Average (Standard dev.)-0.000000000000249 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 945.60004 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_28761_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Ewald sphere corrected map.

Fileemd_28761_additional_1.map
AnnotationEwald sphere corrected map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of ewald sphere corrected Che mutant map.mrc.

Fileemd_28761_half_map_1.map
AnnotationHalf map of ewald sphere corrected Che_mutant_map.mrc.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of ewald sphere corrected Che mutant map.mrc.

Fileemd_28761_half_map_2.map
AnnotationHalf map of ewald sphere corrected Che_mutant_map.mrc.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mycobacterium phage Che8

EntireName: Mycobacterium phage Che8 (virus)
Components
  • Virus: Mycobacterium phage Che8 (virus)

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Supramolecule #1: Mycobacterium phage Che8

SupramoleculeName: Mycobacterium phage Che8 / type: virus / ID: 1 / Parent: 0 / Details: MUTANT. Gene 110 deleted. / NCBI-ID: 2907829 / Sci species name: Mycobacterium phage Che8 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Virus shellShell ID: 1 / Diameter: 730.0 Å / T number (triangulation number): 9

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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

Concentration10 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
10.0 mMC4H11NO3Tris
10.0 mMMgSO4Magnesium sulfate
68.44 mMNaClSodium chloride
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 8118 / 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 / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.39 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 32070
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 3.3.2)
FSC plot (resolution estimation)

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