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    Yorodumi
    - 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 A 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 1, 2010

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    Structure visualization

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

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    Map

    Fileemd_5209.map.gz (map file in CCP4 format, 746497 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    576 pix
    1.95 A/pix
    = 1123.2 A
    576 pix
    1.95 A/pix
    = 1123.2 A
    576 pix
    1.95 A/pix
    = 1123.2 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 1.95 A
    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 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/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
    alpha/beta/gamma90.00090.00090.000
    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/A2 / 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 A / Resolution method: FSC 0.5

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