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- EMDB-8489: Bacteriophage Bellamy -

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Basic information

Entry
Database: EMDB / ID: 8489
TitleBacteriophage Bellamy
Samplebacteriophage Bellamy
Sourcebacteriophage Bellamy / virus
Map dataBacteriophage Bellamy
Methodsingle particle reconstruction, at 30 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: 0.3
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.3
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_8489.map.gz (map file in CCP4 format, 21808 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
176 pix
8.68 Å/pix.
= 1527.68 Å
176 pix
8.68 Å/pix.
= 1527.68 Å
176 pix
8.68 Å/pix.
= 1527.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 8.68 Å
Density
Contour Level:0.3 (by author), 0.3 (movie #1):
Minimum - Maximum-1.4688925 - 2.0571482
Average (Standard dev.)-2.073261E-9 (0.23220612)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions176176176
Origin-88-88-88
Limit878787
Spacing176176176
CellA=B=C: 1527.68 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z8.688.688.68
M x/y/z176176176
origin x/y/z0.0000.0000.000
length x/y/z1527.6801527.6801527.680
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-88-88-88
NC/NR/NS176176176
D min/max/mean-1.4692.057-0.000

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Supplemental data

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Sample components

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Entire bacteriophage Bellamy

EntireName: bacteriophage Bellamy / Number of components: 1

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Component #1: virus, bacteriophage Bellamy

VirusName: bacteriophage Bellamy / Class: VIRION / Empty: Yes / Enveloped: No / Isolate: OTHER
SpeciesSpecies: bacteriophage Bellamy / virus
Source (natural)Host Species: Candidatus synechococcus spongiarum / bacteria / cyanobacteria
Shell #1Name of element: capsid / Diameter: 7800 Å / T number(triangulation number): 13

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 1 mg/ml / pH: 8
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE-PROPANE MIXTURE / Temperature: 293 K / Humidity: 90 %

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 30 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 29000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 5000 nm
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 56 / Sampling size: 6.35 microns

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C5 (5 fold cyclic) / Number of projections: 10600
3D reconstructionSoftware: Auto3DEM / Resolution: 30 Å / Resolution method: OTHER

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