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- EMDB-25155: Non-contracted phage G sheath -

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Basic information

Entry
Database: EMDB / ID: EMD-25155
TitleNon-contracted phage G sheath
Map dataNon-contracted phage G sheath
Sample
  • Virus: Bacillus virus G
Biological speciesBacillus virus G
Methodhelical reconstruction / cryo EM / Resolution: 7.0 Å
AuthorsGonzalez B / Li D / Li K / Hardies SC / Wright ET / Thomas JA / Serwer P / Jiang W
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM132024 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)UA5GM126533 United States
CitationJournal: Viruses / Year: 2021
Title: Structural Studies of the Phage G Tail Demonstrate an Atypical Tail Contraction
Authors: Gonzalez B / Li D / Li K / Wright ET / Hardies SC / Thomas JA / Serwer P / Jiang W
History
DepositionOct 16, 2021-
Header (metadata) releaseNov 17, 2021-
Map releaseNov 17, 2021-
UpdateNov 17, 2021-
Current statusNov 17, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.573
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.573
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_25155.png

Downloads & links

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Map

FileDownload / File: emd_25155.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNon-contracted phage G sheath
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.48 Å/pix.
x 224 pix.
= 780.416 Å		3.48 Å/pix.
x 224 pix.
= 780.416 Å		3.48 Å/pix.
x 224 pix.
= 780.416 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.484 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.573 / Movie #1: 0.573
Minimum - Maximum-1.3433125 - 2.325486
Average (Standard dev.)0.014586222 (±0.114460826)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 780.416 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.4843.4843.484
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z780.416780.416780.416
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS224224224
D min/max/mean-1.3432.3250.015

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Supplemental data

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Sample components

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Entire : Bacillus virus G

EntireName: Bacillus virus G
Components
  • Virus: Bacillus virus G

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Supramolecule #1: Bacillus virus G

SupramoleculeName: Bacillus virus G / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 1084719 / Sci species name: Bacillus virus G / 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
Processinghelical reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 375 / Average electron dose: 14.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 41.53 Å
Applied symmetry - Helical parameters - Δ&Phi: 20.570 °
Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2099
Segment selectionNumber selected: 22755 / Software - Name: RELION
Startup modelType of model: NONE / Details: Ab-initio modeling using CryoSPARC
Final angle assignmentType: NOT APPLICABLE

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