|Entry||Database: EMDB / ID: 1864|
|Title||Cryo-EM reconstruction of native and expanded Turnip Crinkle virus|
|Keywords||Turnip crinkle virus / genomic RNA structure / genome uncoating / ssRNA virus|
|Sample||Turnip crinkle virus|
|Source||Turnip crinkle virus / virus|
|Map data||3D cryo-EM reconstruction of the expanded form of Turnip Crinkle Virus|
|Method||single particle (icosahedral) reconstruction, at 17 Å resolution|
|Authors||Bakker SE / Robottom J / Pearson AR / Stockley PG / Ranson NA|
|Citation||J. Mol. Biol., 2012, 417, 65-78|
primary. J. Mol. Biol., 2012, 417, 65-78 Yorodumi Papers
|Validation Report||PDB-ID: 3zx9|
SummaryFull reportAbout validation report
|Date||Deposition: Jan 25, 2011 / Header (metadata) release: Jul 9, 2012 / Map release: Jul 9, 2012 / Last update: Apr 30, 2014|
Downloads & links
|File||emd_1864.map.gz (map file in CCP4 format, 54001 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.89 Å|
CCP4 map header:
-Entire Turnip crinkle virus
|Entire||Name: Turnip crinkle virus / Number of components: 1 / Oligomeric State: Icosahedral virus|
|Mass||Theoretical: 6.8 MDa|
-Component #1: virus, Turnip crinkle virus
|Virus||Name: Turnip crinkle virus / a.k.a: Turnip crinkle virus / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN|
|Mass||Theoretical: 6.8 MDa|
|Species||Species: Turnip crinkle virus / virus|
|Source (natural)||Host Species: Brassica rapa subsp. rapa / plant / image: Brassica rapa|
|Shell #1||Name of element: Expanded / Diameter: 380 Å / T number(triangulation number): 3|
|Sample solution||Specimen conc.: 3 mg/ml / Buffer solution: 100 mM Tris pH 8.5, 5 mM EDTA / pH: 8.5|
|Support film||400 mesh copper grid|
|Vitrification||Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 77 K / Method: Blot 1.6 seconds before plunging|
Details: Vitrification instrument: Double sided automated blotter and plunger
-Electron microscopy imaging
Model: Tecnai F20 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F20|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 50000 X (nominal), 52911 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 3500 nm|
|Specimen Holder||Holder: Gatan 626 / Model: GATAN LIQUID NITROGEN|
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 41 / Scanner: OTHER / Sampling size: 10 microns|
|Processing||Method: single particle (icosahedral) reconstruction / Number of projections: 5121 / Number of class averages: 110 / Applied symmetry: I (icosahedral)|
|3D reconstruction||Algorithm: Icosahedral / Software: SPIDER / CTF correction: Phase-flipping each particle / Resolution: 17 Å / Resolution method: FSC 0.5|
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