Movie controller

-

    -

    -


    Orientation:

    Jmol status

    -

    -
    Mouse picking

    ID:- Chain:- Residue:- Atom:-
    [English] 日本語
    Yorodumi
    - EMDB-1680: Macromolecular crystal data phased by negative staining electron ... -

    +
    Open data

    ID or keywords:

    Loading...

    no data

    -
    Basic information

    Entry
    Database: EMDB / ID: 1680
    TitleMacromolecular crystal data phased by negative staining electron microscopy reconstructions
    KeywordsNegative staining / electron microscopy / reconstructions / phasing
    SampleType-II dehydroquinase (DHQ) from Candida albicans (CaDHQ)
    SourceCandida albicans / yeast
    Map dataMacromolecular crystal data phased by negative staining electron microscopy reconstructions as a proof of principle
    Methodsingle particle reconstruction, at 15 A resolution
    AuthorsTrapani S / Schoehn G / Navaza J / Abergel C
    CitationActa Crystallogr. D Biol. Crystallogr., 2010, 66, 514-521

    Acta Crystallogr. D Biol. Crystallogr., 2010, 66, 514-521 StrPapers
    Macromolecular crystal data phased by negative-stained electron-microscopy reconstructions.
    Stefano Trapani / Guy Schoehn / Jorge Navaza / Chantal Abergel

    DateDeposition: Jan 13, 2010 / Header (metadata) release: Jan 18, 2010 / Map release: Jan 28, 2011 / Last update: Jan 13, 2010

    -
    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 165
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view colored by radius
    • Surface level: 165
    • Imaged by UCSF CHIMERA
    • Download
    3D viewer /

    View / / Stereo:
    Center
    Zoom
    Scale
    slabnear <=> far

    fix: /
    Orientation
    Orientation Rotation
    misc. /
    Show/hide
    Supplemental images

    Downloads & links

    -
    Map

    Fileemd_1680.map.gz (map file in CCP4 format, 2574 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    87 pix
    1.4 A/pix
    = 121.8 A
    87 pix
    1.4 A/pix
    = 121.8 A
    87 pix
    1.4 A/pix
    = 121.8 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 1.4 A
    Density
    Contour Level:165 (by emdb), 165 (movie #1):
    Minimum - Maximum-335 - 426.472
    Average (Standard dev.)31.2115 (113.128)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions878787
    Origin000
    Limit868686
    Spacing878787
    CellA=B=C: 121.8 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z1.41.41.4
    M x/y/z878787
    origin x/y/z0.0000.0000.000
    length x/y/z121.800121.800121.800
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ000
    NX/NY/NZ121121121
    MAP C/R/S123
    start NC/NR/NS000
    NC/NR/NS878787
    D min/max/mean-335.000426.47231.212

    -
    Supplemental data

    -
    Sample components

    -
    Entire Type-II dehydroquinase (DHQ) from Candida albicans (CaDHQ)

    EntireName: Type-II dehydroquinase (DHQ) from Candida albicans (CaDHQ)
    Number of components: 1 / Oligomeric State: Dodecamer
    MassExperimental: 200 kDa

    -
    Component #1: protein, CaDHQ

    ProteinName: CaDHQ / a.k.a: CaDHQ / Oligomeric Details: Dodecamer / Recombinant expression: Yes / Number of Copies: 12
    MassTheoretical: 17 kDa
    SourceSpecies: Candida albicans / yeast
    Source (engineered)Expression System: Escherichia coli / bacteria /

    +
    Experimental details

    -
    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 0.05 mg/ml / Buffer solution: 20mM NaCl, 10mM Tris-HCL / pH: 7.4
    Support film400 mesk copper grid
    StainingNegative staining using 1% methylamine vanadate, CH3NH2VO3
    VitrificationInstrument: NONE / Cryogen name: NONE / Details: Negative staining at room temperature

    -
    Electron microscopy imaging

    ImagingMicroscope: JEOL 1200EXII / Date: Dec 12, 2006 / Details: Low dose negative staining
    Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 100 kV / Illumination mode: OTHER
    LensMagnification: 50000 X (nominal)
    Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
    Imaging mode: BRIGHT FIELD / Defocus: 1000 - 2500 nm
    Specimen HolderHolder: Eucentric / Model: JEOL
    CameraDetector: KODAK SO-163 FILM

    -
    Image acquisition

    Image acquisitionNumber of digital images: 8 / Scanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 8

    -
    Image processing

    ProcessingMethod: single particle reconstruction / Number of class averages: 114 / Number of projections: 7200 / Applied symmetry: T (tetrahedral)
    3D reconstructionAlgorithm: Back projection / Software: Spider / CTF correction: Each negative
    Details: 7200 particles included in the reconstruction (out of 12000). 432 symmetry imposed
    Resolution: 15 A / Resolution method: FSC 0.5

    +
    About Yorodumi

    -
    News

    -
    Sep 15, 2016. EM Navigator & Yorodumi renewed

    EM Navigator & Yorodumi renewed

    • New versions of EM Navigator and Yorodumi started

    Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

    -
    Aug 31, 2016. New EM Navigator & Yorodumi

    New EM Navigator & Yorodumi

    • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
    • Current version will continue as 'legacy version' for some time.

    Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

    +
    Apr 13, 2016. Omokage search got faster

    Omokage search got faster

    • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
    • Enjoy "shape similarity" of biomolecules, more!

    Related info.: Omokage search

    +
    Mar 3, 2016. Presentation (PDF format) at IPR seminar on Feb 19.

    Read more

    -
    Yorodumi

    Thousand views of thousand structures

    • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
    • All the functionalities will be ported from the levgacy version.
    • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

    Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

    Read more