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- EMDB-1557: Cryo-EM density map of Epsilon-15 bacteriophage icosahedral recon... -

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Basic information

Entry
Database: EMDB / ID: EMD-1557
TitleCryo-EM density map of Epsilon-15 bacteriophage icosahedral reconstruction from JADAS automatically acquired data at 7.3 Angstrom resolution.
Map dataThis is the density map of the epsilon-15 bacteriophage reconstructed from JADAS automatically acquired images.
Sample
  • Sample: Epsilon-15 bacteriophage
  • Virus: Salmonella phage epsilon15 (virus)
KeywordsSingle-particle / Automated data collection / Reconstruction / Cryo-EM / Epsilon-15 bacteriophage
Biological speciesSalmonella phage epsilon15 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.3 Å
AuthorsZhang J / Nakamura N / Shimizu Y / Liang N / Liu X / Jakana J / Marsh MP / Booth CR / Shinkawa T / Nakata M / Chiu W
CitationJournal: J Struct Biol / Year: 2009
Title: JADAS: a customizable automated data acquisition system and its application to ice-embedded single particles.
Authors: Junjie Zhang / Natsuko Nakamura / Yuko Shimizu / Nathan Liang / Xiangan Liu / Joanita Jakana / Michael P Marsh / Christopher R Booth / Takao Shinkawa / Munetaka Nakata / Wah Chiu /
Abstract: The JEOL Automated Data Acquisition System (JADAS) is a software system built for the latest generation of the JEOL Transmission Electron Microscopes. It is designed to partially or fully automate ...The JEOL Automated Data Acquisition System (JADAS) is a software system built for the latest generation of the JEOL Transmission Electron Microscopes. It is designed to partially or fully automate image acquisition for ice-embedded single particles under low dose conditions. Its built-in flexibility permits users to customize the order of various imaging operations. In this paper, we describe how JADAS is used to accurately locate and image suitable specimen areas on a grid of ice-embedded particles. We also demonstrate the utility of JADAS by imaging the epsilon 15 bacteriophage with the JEM3200FSC electron cryo-microscope, showing that sufficient images can be collected in a single 8h session to yield a subnanometer resolution structure which agrees with the previously determined structure.
History
DepositionSep 8, 2008-
Header (metadata) releaseSep 12, 2008-
Map releaseApr 29, 2009-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.2
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1557.jpg

Downloads & links

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Map

FileDownload / File: emd_1557.map.gz / Format: CCP4 / Size: 173.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the density map of the epsilon-15 bacteriophage reconstructed from JADAS automatically acquired images.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.62 Å/pix.
x 360 pix.
= 943.2 Å		2.62 Å/pix.
x 360 pix.
= 943.2 Å		2.62 Å/pix.
x 360 pix.
= 943.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.62 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.6 / Movie #1: 1.2
Minimum - Maximum-2.05162 - 4.17608
Average (Standard dev.)0.0414809 (±0.320718)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-180-180-180
Dimensions360360360
Spacing360360360
CellA=B=C: 943.2 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.622.622.62
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z943.200943.200943.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-81-81-81
NX/NY/NZ160160160
MAP C/R/S123
start NC/NR/NS-180-180-180
NC/NR/NS360360360
D min/max/mean-2.0524.1760.041

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Supplemental data

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Sample components

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Entire : Epsilon-15 bacteriophage

EntireName: Epsilon-15 bacteriophage
Components
  • Sample: Epsilon-15 bacteriophage
  • Virus: Salmonella phage epsilon15 (virus)

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Supramolecule #1000: Epsilon-15 bacteriophage

SupramoleculeName: Epsilon-15 bacteriophage / type: sample / ID: 1000
Details: The sample is frozen on carbon support film in vitreous ice.
Number unique components: 1
Molecular weightExperimental: 22 MDa / Theoretical: 22 MDa

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Supramolecule #1: Salmonella phage epsilon15

SupramoleculeName: Salmonella phage epsilon15 / type: virus / ID: 1 / Name.synonym: Epsilon-15 bacteriophage
Details: The sample is frozen on carbon support film in vitreous ice.
NCBI-ID: 215158 / Sci species name: Salmonella phage epsilon15 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: Epsilon-15 bacteriophage
Host (natural)Organism: Salmonella (bacteria) / synonym: BACTERIA(EUBACTERIA)
Molecular weightExperimental: 22 MDa / Theoretical: 22 MDa
Virus shellShell ID: 1 / T number (triangulation number): 7

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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

GridDetails: 400 mesh copper grid with holy carbon film
VitrificationCryogen name: ETHANE / Instrument: OTHER

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Electron microscopy

MicroscopeJEOL 3200FSC
TemperatureAverage: 100 K
Specialist opticsEnergy filter - Name: JEOL in-column omega filter
DetailsData is automatically collected using JEOL Automated Data Acquisition System (JADAS). Microscope used JEM3200FSC
Image recordingCategory: CCD / Film or detector model: GENERIC GATAN (4k x 4k) / Digitization - Sampling interval: 2.62 µm / Number real images: 181 / Average electron dose: 20 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 56680 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal magnification: 40000
Sample stageSpecimen holder: JEM3200FSC cryoholder / Specimen holder model: OTHER

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Image processing

CTF correctionDetails: Each CCD image
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.3 Å / Resolution method: OTHER / Software - Name: Multi-path simulated annealing / Number images used: 7543

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