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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: 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.
SampleEpsilon-15 bacteriophage:
virus
KeywordsSingle-particle / Automated data collection / Reconstruction / Cryo-EM / Epsilon-15 bacteriophage
SourceSalmonella phage epsilon15 (bacteriophage)
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.
P-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.
DateDeposition: Sep 8, 2008 / Header (metadata) release: Sep 12, 2008 / Map release: Apr 29, 2009 / Last update: Oct 24, 2012

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Strvis

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
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downlink

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Map

Fileemd_1557.map.gz (map file in CCP4 format, 182251 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
360 pix
2.62 Å/pix.
= 943.2 Å
360 pix
2.62 Å/pix.
= 943.2 Å
360 pix
2.62 Å/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
Contour Level:1.6 (by author), 1.2 (movie #1):
Minimum - Maximum-2.05162 - 4.17608
Average (Standard dev.)0.0414809 (0.320718)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions360360360
Origin-180-180-180
Limit179179179
Spacing360360360
CellA=B=C: 943.2 Å
α=β=γ: 90 deg.

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
Details: The sample is frozen on carbon support film in vitreous ice.
Number of components: 1
MassTheoretical: 22 MDa / Experimental: 22 MDa

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Component #1: virus, Salmonella phage epsilon15

VirusName: Salmonella phage epsilon15 / a.k.a: Epsilon-15 bacteriophage / Class: VIRION
Details: The sample is frozen on carbon support film in vitreous ice.
Empty: No / Enveloped: No / Isolate: STRAIN
MassTheoretical: 22 MDa / Experimental: 22 MDa
SpeciesSpecies: Salmonella phage epsilon15 (bacteriophage)
Source (natural)Host Species: Salmonella (bacteria) / Host category: BACTERIA(EUBACTERIA)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Support film400 mesh copper grid with holy carbon film
VitrificationInstrument: NONE / Cryogen name: ETHANE

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Electron microscopy imaging

ImagingMicroscope: JEOL 3200FSC
Details: Data is automatically collected using JEOL Automated Data Acquisition System (JADAS). Microscope used JEM3200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 40000 X (nominal), 56680 X (calibrated) / Cs: 4.1 mm / Imaging mode: BRIGHT FIELD / Energy filter: JEOL in-column omega filter
Specimen HolderHolder: JEM3200FSC cryoholder / Model: OTHER / Temperature: 100 K
CameraDetector: GENERIC GATAN (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 181 / Sampling size: 2.62 microns / Bit depth: 8

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 7543 / Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: Cross-common lines / Software: Multi-path simulated annealing / CTF correction: Each CCD image / Resolution: 7.3 Å
Resolution method: FSC at 0.5 with our previously published data

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