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    Yorodumi
    - EMDB-2050: Capsid structure and its Stability at the Late Stages of Bacterio... -

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    Basic information

    Entry
    Database: EMDB / ID: 2050
    TitleCapsid structure and its Stability at the Late Stages of Bacteriophage SPP1 Assembly
    KeywordsBacteriophage Capsid SPP1
    SampleCapsid of SPP1 lacking the auxiliary protein gp12
    SourceBacillus phage SPP1 / virus / image: Bacillus subtilis
    Map dataReconstruction of an SPP1 capsid that lacks the auxillary protein gp12
    Methodsingle particle (icosahedral) reconstruction, at 15.1 A resolution
    AuthorsWhite HE / Sherman MB / Brasiles S / Jacquet E / Seavers P / Tavares P / Orlova EV
    CitationJ. Virol., 2012, 86, 6768-6777

    J. Virol., 2012, 86, 6768-6777 StrPapers
    Capsid structure and its stability at the late stages of bacteriophage SPP1 assembly.
    Helen E White / Michael B Sherman / Sandrine Brasilès / Eric Jacquet / Philippa Seavers / Paulo Tavares / Elena V Orlova

    DateDeposition: Mar 14, 2012 / Header (metadata) release: Mar 16, 2012 / Map release: Jun 14, 2012 / Last update: Mar 14, 2012

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    Structure visualization

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    • Surface view with section colored by density value
    • Surface level: 5
    • Imaged by UCSF CHIMERA
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    • Surface view colored by radius
    • Surface level: 5
    • Imaged by UCSF CHIMERA
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    Map

    Fileemd_2050.map.gz (map file in CCP4 format, 524289 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    512 pix
    1.49 A/pix
    = 762.88 A
    512 pix
    1.49 A/pix
    = 762.88 A
    512 pix
    1.49 A/pix
    = 762.88 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 1.49 A
    Density
    Contour Level:5 (by author), 5 (movie #1):
    Minimum - Maximum-22.61569023 - 28.6905098
    Average (Standard dev.)-1E-8 (3.00000048)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions512512512
    Origin-255-256-256
    Limit256255255
    Spacing512512512
    CellA=B=C: 762.88 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z1.491.491.49
    M x/y/z512512512
    origin x/y/z0.0000.0000.000
    length x/y/z762.880762.880762.880
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-184-184-183
    NX/NY/NZ368368368
    MAP C/R/S123
    start NC/NR/NS-256-255-256
    NC/NR/NS512512512
    D min/max/mean-22.61628.691-0.000

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    Supplemental data

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    Sample components

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    Entire Capsid of SPP1 lacking the auxiliary protein gp12

    EntireName: Capsid of SPP1 lacking the auxiliary protein gp12 / Number of components: 1 / Oligomeric State: Icosahedron

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    Component #1: virus, Bacillus phage SPP1

    VirusName: Bacillus phage SPP1 / Class: OTHER / Empty: No / Enveloped: No / Isolate: SPECIES
    SpeciesSpecies: Bacillus phage SPP1 / virus / image: Bacillus subtilis
    Source (natural)Host Species: Bacillus subtilis / bacteria / / Host category: BACTERIA(EUBACTERIA)

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Support filmholey carbon film grids
    VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE

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    Electron microscopy imaging

    ImagingMicroscope: JEOL 2200FS / Date: Mar 1, 2010 / Details: low-dose imaging procedure
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 20 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 50000 X (nominal) / Imaging mode: BRIGHT FIELD
    Specimen HolderModel: GATAN LIQUID NITROGEN
    CameraDetector: GENERIC CCD

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    Image processing

    ProcessingMethod: single particle (icosahedral) reconstruction / Number of projections: 3200 / Applied symmetry: I (icosahedral)
    3D reconstructionAlgorithm: Angular reconstitution / Software: Imagic / CTF correction: Phase flipping / Resolution: 15.1 A / Resolution method: FSC 0.5

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