|Entry||Database: EMDB / ID: 1996|
|Title||Bubblegrams reveal the inner body of bacteriophage phiKZ|
|Keywords||inner body / core protein / asymmetric reconstruction / phiKZ / protein mapping|
|Sample||phiKZ mature phage|
|Source||Pseudomonas phage phiKZ / virus / phiKZ|
|Map data||This is the inner body structure of bacteriophage phiKZ.|
|Method||single particle reconstruction, at 37 Å resolution|
|Authors||Wu W / Thomas JA / Cheng N / Black LW / Steven AC|
|Citation||Science, 2012, 335, 182-182|
|Date||Deposition: Nov 23, 2011 / Header (metadata) release: Jan 13, 2012 / Map release: Jan 13, 2012 / Last update: Sep 26, 2012|
Downloads & links
|File||emd_1996.map.gz (map file in CCP4 format, 16001 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 10.026 Å|
CCP4 map header:
-Entire phiKZ mature phage
|Entire||Name: phiKZ mature phage / Number of components: 5|
Oligomeric State: Inner body inside the capsid surrounding by DNA
-Component #1: virus, Pseudomonas phage phiKZ
|Vitrification||Instrument: NONE / Cryogen name: ETHANE / Temperature: 100 K / Humidity: 40 %|
-Electron microscopy imaging
|Imaging||Microscope: FEI/PHILIPS CM200FEG / Date: Jan 20, 2011|
Details: Image pairs. First low dose image, 12 electrons per angstrom squared, then high dose to get radiation damage (same dose but longer time), dose about 5-fold of low dose.
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 12 e/Å2 / Illumination mode: SPOT SCAN|
|Lens||Magnification: 38000 X (nominal), 38000 X (calibrated) / Astigmatism: condenser and objective lens astigmatism / Cs: 2 mm / Imaging mode: OTHER / Defocus: 800 - 1500 nm|
|Specimen Holder||Holder: Eucentric / Model: GATAN LIQUID NITROGEN / Temperature: 100 K|
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 95 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 6.35 microns / Bit depth: 16|
|Processing||Method: single particle reconstruction / Number of projections: 2775 / Applied symmetry: C1 (asymmetric)|
|3D reconstruction||Algorithm: Projection match / Software: EMAN / CTF correction: Micrograph|
Details: Projection match method was used to determine the unique vertex and the orientation of tail. The inner body was solved directly from 2D data without using any initial model.
Resolution: 37 Å / Resolution method: FSC 0.5
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- Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
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