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- EMDB-8484: Bacteriophage G -

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Basic information

Entry
Database: EMDB / ID: 8484
TitleBacteriophage G
Samplebacteriophage G
Sourcebacteriophage G / virus
Map dataBacteriophage G
Methodsingle particle reconstruction, at 15 Å resolution
AuthorsHua J / Huet A / Lopez CA / Toropova K / Pope WH / Duda RL / Hendrix RW / Conway JF
CitationMBio, 2017, 8

MBio, 2017, 8 Yorodumi Papers
Capsids and Genomes of Jumbo-Sized Bacteriophages Reveal the Evolutionary Reach of the HK97 Fold.
Jianfei Hua / Alexis Huet / Carlos A Lopez / Katerina Toropova / Welkin H Pope / Robert L Duda / Roger W Hendrix / James F Conway

DateDeposition: Nov 29, 2016 / Header (metadata) release: Feb 8, 2017 / Map release: Nov 1, 2017 / Last update: Nov 1, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 7
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 7
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_8484.map.gz (map file in CCP4 format, 868328 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
601 pix
3.58 Å/pix.
= 2151.58 Å
601 pix
3.58 Å/pix.
= 2151.58 Å
601 pix
3.58 Å/pix.
= 2151.58 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 3.58 Å
Density
Contour Level:7 (by author), 7 (movie #1):
Minimum - Maximum-19.817001 - 32.443
Average (Standard dev.)0.56182224 (3.909054)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions601601601
Origin000
Limit600600600
Spacing601601601
CellA=B=C: 2151.5798 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.583.583.58
M x/y/z601601601
origin x/y/z0.0000.0000.000
length x/y/z2151.5802151.5802151.580
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS601601601
D min/max/mean-19.81732.4430.562

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Supplemental data

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Sample components

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Entire bacteriophage G

EntireName: bacteriophage G / Number of components: 1

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Component #1: virus, bacteriophage G

VirusName: bacteriophage G / Class: VIRION / Empty: No / Enveloped: No / Isolate: OTHER
SpeciesSpecies: bacteriophage G / virus
Source (natural)Host Species: Bacillus megaterium / bacteria / バチルス・メガテリウム / image: Bacillus subtilis
Shell #1Name of element: capsid / Diameter: 1600 Å / T number(triangulation number): 52

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 1 mg/ml / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE-PROPANE MIXTURE / Temperature: 293 K / Humidity: 90 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 30 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 78000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 5000 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 204 / Sampling size: 14 microns

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 344
3D reconstructionSoftware: Auto3DEM / Resolution: 15 Å / Resolution method: FSC 0.5 CUT-OFF
FSC plot (resolution assessment)

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