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- EMDB-5209: Epsilon15 asymmetric reconstruction using conventional cryo-EM -

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Basic information

Entry
Database: EMDB / ID: 5209
TitleEpsilon15 asymmetric reconstruction using conventional cryo-EM
KeywordsElectron microscopy / phase plate / Bacteriophage / epsilon15
SampleEpsilon15
SourceEpsilon15 / bacteriophage
Map dataasymmetric reconstruction of epsilon15 from conventional cryoEM particles
Methodsingle particle reconstruction, at 13 Å resolution
AuthorsMurata K / Liu X / Danev R / Jakana J / Schmid MF / King J / Nagayama K / Chiu W
CitationStructure, 2010, 18, 903-912

Structure, 2010, 18, 903-912 StrPapers
Zernike phase contrast cryo-electron microscopy and tomography for structure determination at nanometer and subnanometer resolutions.
Kazuyoshi Murata / Xiangan Liu / Radostin Danev / Joanita Jakana / Michael F Schmid / Jonathan King / Kuniaki Nagayama / Wah Chiu

DateDeposition: Jul 1, 2010 / Header (metadata) release: Jul 19, 2010 / Map release: Sep 1, 2010 / Last update: Jul 8, 2011

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_5209.map.gz (map file in CCP4 format, 746497 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
576 pix
1.95 Å/pix.
= 1123.2 Å
576 pix
1.95 Å/pix.
= 1123.2 Å
576 pix
1.95 Å/pix.
= 1123.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.95 Å
Density
Contour Level:1 (by author), 1 (movie #1):
Minimum - Maximum-1.46255 - 3.10983
Average (Standard dev.)0.0642926 (0.252498)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions576576576
Origin-288-288-288
Limit287287287
Spacing576576576
CellA=B=C: 1123.2 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.951.951.95
M x/y/z576576576
origin x/y/z0.0000.0000.000
length x/y/z1123.2001123.2001123.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-99-99-99
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS-288-288-288
NC/NR/NS576576576
D min/max/mean-1.4633.1100.064

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Supplemental data

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Sample components

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Entire Epsilon15

EntireName: Epsilon15 / Details: The sample was monodisperse / Number of components: 6
MassTheoretical: 500 kDa

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Component #1: virus, epsilon15

VirusName: epsilon15 / a.k.a: bacteriophage / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Epsilon15 / bacteriophage
Source (natural)Host Species: Salmonella / bacteria / Host category: BACTERIA(EUBACTERIA)

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionBuffer solution: 10 mM Tris pH7.5, 25 mM NaCl and 5 mM MgCl2
pH: 7.5
Support filmQuantifoil R2/2 grid
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Method: Blot for 2 seconds before plunging / Details: Vitrification instrument: vitrobot

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Electron microscopy imaging

ImagingMicroscope: JEOL 2200FS / Date: Dec 1, 2009 / Details: Weak beam illumination
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 75000 X (nominal), 75000 X (calibrated) / Cs: 4.3 mm / Imaging mode: BRIGHT FIELD / Energy filter: JEOL / Energy window: 0-20 eV
Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN / Temperature: 90 K
CameraDetector: GENERIC TVIPS (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 722 / Bit depth: 16

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 17800
Details: The particles were selected using the consistency criterion of MPSA
Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: Cross-common lines / Software: MPSA / CTF correction: each micrograph / Details: the map was reconstructed with ctf correction. / Resolution: 13 Å / Resolution method: FSC 0.5

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