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    Yorodumi
    - EMDB-5242: B. subtilis RNase P RNA Specificity domain folding intermediate -

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    Basic information

    Entry
    Database: EMDB / ID: 5242
    TitleB. subtilis RNase P RNA Specificity domain folding intermediate
    KeywordsRNA folding intermediate RNase P Specificity domain
    SampleB. subtilis RNase P RNA Specificity domain folding intermediate
    SourceBacillus subtilis / bacteria /
    Map dataThis is a map of the folding intermediate of B. subtilis RNase P Specificity domain
    Methodsingle particle reconstruction, at 15.2 A resolution
    AuthorsBaird NJ / Ludtke SJ / Khant H / Chiu W / Pan T / Sosnick TR
    CitationJ. Am. Chem. Soc., 2010, 132, 16352-16353

    J. Am. Chem. Soc., 2010, 132, 16352-16353 StrPapers
    Discrete structure of an RNA folding intermediate revealed by cryo-electron microscopy.
    Nathan J Baird / Steven J Ludtke / Htet Khant / Wah Chiu / Tao Pan / Tobin R Sosnick

    DateDeposition: Oct 27, 2010 / Header (metadata) release: Dec 22, 2010 / Map release: Dec 22, 2010 / Last update: Oct 27, 2010

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 0.0623
    • Imaged by UCSF CHIMERA
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    • Surface view colored by radius
    • Surface level: 0.0623
    • Imaged by UCSF CHIMERA
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    Supplemental images

    Downloads & links

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    Map

    Fileemd_5242.map.gz (map file in CCP4 format, 16001 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    160 pix
    1.81 A/pix
    = 289.6 A
    160 pix
    1.81 A/pix
    = 289.6 A
    160 pix
    1.81 A/pix
    = 289.6 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 1.81 A
    Density
    Contour Level:0.0623 (by author), 0.0623 (movie #1):
    Minimum - Maximum-0.08578543 - 2.46069574
    Average (Standard dev.)0.00539513 (0.07407818)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions160160160
    Origin-80-80-80
    Limit797979
    Spacing160160160
    CellA=B=C: 289.59998 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z1.811.811.81
    M x/y/z160160160
    origin x/y/z0.0000.0000.000
    length x/y/z289.600289.600289.600
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-62-62-62
    NX/NY/NZ125125125
    MAP C/R/S123
    start NC/NR/NS-80-80-80
    NC/NR/NS160160160
    D min/max/mean-0.0862.4610.005

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    Supplemental data

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    Sample components

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    Entire B. subtilis RNase P RNA Specificity domain folding intermediate

    EntireName: B. subtilis RNase P RNA Specificity domain folding intermediate
    Details: none / Number of components: 1 / Oligomeric State: Monomer of Specificity domain
    MassTheoretical: 50 kDa
    Measured by: Calculation from nucleotide sequence, 154mer RNA

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    Component #1: nucleic-acid, RNA

    Nucleic-acidName: RNA / a.k.a: RNase P RNA Specificity domain / Class: RNA / Structure: OTHER
    Sequence:
    GCGAGCCUAG CGAAGUCAUA AGCUAGGGCA GUCUUUAGAG GCUGACGGCA GGAAAAAAGC CUACGUCUUC GGAUAUGGCU GAGUAUCCUU GAAAGUGCCA CAGUGACGAA GUCUCACUAG AAAUGGUGAG AGUGGAACGC GGUAAACCCC UCGC

    Synthetic: No
    MassTheoretical: 50 kDa
    SourceSpecies: Bacillus subtilis / bacteria /

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 1 mg/ml / Buffer solution: 1 mM MgCl2, 20 mM TrisHCl pH 8 / pH: 8
    Support film400 mesh carbon grid
    VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 77 K / Humidity: 100 % / Method: 2 blots 1 second each before plunging / Details: Vitrification instrument: FEI Vitrobot mark III

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    Electron microscopy imaging

    ImagingMicroscope: JEOL 2010F / Date: Mar 10, 2006
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 16 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 60000 X (nominal)
    Astigmatism: object astigmatism correction made at 400,000 times magnification
    Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 3500 nm
    Specimen HolderHolder: single tilt cryo-holder / Model: GATAN LIQUID NITROGEN / Temperature: 94.1 K ( 93 - 95 K)
    CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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    Image acquisition

    Image acquisitionNumber of digital images: 100

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of class averages: 60 / Number of projections: 11600
    Details: The particles were selected using an automatic selection program and then inspected manually
    Applied symmetry: C1 (asymmetric)
    3D reconstructionAlgorithm: Cross-common lines / Software: EMAN
    Details: FSC gives a resolution of 15.2 A, but the model was low-pass filtered to 26 A, corresponding to the first zero-crossing of the data. CTF correction was not performed.
    Resolution: 15.2 A / Resolution method: FSC 0.5

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