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    Yorodumi
    - EMDB-5124: Cryo-EM of Rift Valley fever virus -

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    Basic information

    Entry
    Database: EMDB / ID: 5124
    TitleCryo-EM of Rift Valley fever virus
    Keywordscryo-electron microscopy / single particle averaging / Rift valley fever / bunyaviridae / inter-capsomer contacts
    SampleRift Valley fever virus, RVFV vaccine strain MP-12
    SourceRift Valley fever virus / virus / RVFV
    Map datathis is RVFV map in 2-fold orientation
    Methodsingle particle (icosahedral) reconstruction, at 27 A resolution
    AuthorsSherman MB / Freiberg AN / Holbrook AM / Watowich SJ
    CitationVirology, 2009, 387, 11-15

    primary. Virology, 2009, 387, 11-15 StrPapers
    Single-particle cryo-electron microscopy of Rift Valley fever virus.
    Michael B Sherman / Alexander N Freiberg / Michael R Holbrook / Stanley J Watowich

    1. J.VIROL., 2008, 82, 10341-10348
    Three-dimensional organization of Rift Valley fever virus revealed by cryoelectron tomography
    Freiberg AN / Sherman MB / Morais MC / Holbrook MR / Watowich SJ

    DateDeposition: Jul 20, 2009 / Header (metadata) release: Jul 24, 2009 / Map release: Jul 24, 2009 / Last update: Jul 20, 2009

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 7.3
    • Imaged by UCSF CHIMERA
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    • Surface view colored by radius
    • Surface level: 7.3
    • Imaged by UCSF CHIMERA
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    Supplemental images

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    Map

    Fileemd_5124.map.gz (map file in CCP4 format, 358337 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    451 pix
    3 A/pix
    = 1353. A
    451 pix
    3 A/pix
    = 1353. A
    451 pix
    3 A/pix
    = 1353. A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 3 A
    Density
    Contour Level:6 (by author), 7.3 (movie #1):
    Minimum - Maximum-26.2832 - 37.4125
    Average (Standard dev.)0.675954 (6.08815)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions451451451
    Origin-225-225-225
    Limit225225225
    Spacing451451451
    CellA=B=C: 1353 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z333
    M x/y/z451451451
    origin x/y/z0.0000.0000.000
    length x/y/z1353.0001353.0001353.000
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-34-26-72
    NX/NY/NZ6953145
    MAP C/R/S123
    start NC/NR/NS-225-225-225
    NC/NR/NS451451451
    D min/max/mean-26.28337.4120.676

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    Supplemental data

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    Sample components

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    Entire Rift Valley fever virus, RVFV vaccine strain MP-12

    EntireName: Rift Valley fever virus, RVFV vaccine strain MP-12 / Details: monodisperse sample / Number of components: 8 / Oligomeric State: single virions

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    Component #1: virus, Rift Valley fever virus

    VirusName: Rift Valley fever virus / a.k.a: RVFV / Class: VIRION / Details: 100 nm particles / Empty: No / Enveloped: Yes / Isolate: STRAIN
    SpeciesSpecies: Rift Valley fever virus / virus / RVFV
    Source (natural)Host Species: Homo sapiens / human / Host category: VERTEBRATES

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 0.1 mg/ml / Buffer solution: 10 mM Tris-HCl, 100 mM NaCl, 1 mM EDTA / pH: 7.2
    Support film200 mesh copper Qauntifoil grids
    VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 95 K / Humidity: 80 % / Method: blot 2 sec before plunging / Details: Vitrification instrument: pneumatic plunger

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    Electron microscopy imaging

    ImagingMicroscope: JEOL 2200FS / Date: Nov 1, 2007
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 20 e/A2 / Electron beam tilt params: 0 / Illumination mode: FLOOD BEAM
    LensMagnification: 40000 X (nominal), 40200 X (calibrated)
    Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
    Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 700 - 3700 nm / Energy filter: omega / Energy window: 0-20 eV
    Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN / Temperature: 99 K ( 99 - 99 K)
    CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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    Image acquisition

    Image acquisitionNumber of digital images: 93 / Sampling size: 14 microns / Bit depth: 16

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    Image processing

    ProcessingMethod: single particle (icosahedral) reconstruction / Number of projections: 108 / Number of class averages: 1 / Applied symmetry: I (icosahedral)
    3D reconstructionAlgorithm: PFT / Software: PFT / CTF correction: Each particle / Details: Final map calculated from 108 particles / Resolution: 27 A / Resolution method: FSC

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