|Entry||Database: EMDB / ID: 5383|
|Title||Marine Bacteriophage SIO-2 with T12 symmetry (Procapsid)|
|Keywords||procapsid / Marine Bacteriophage / Phage / Virus / Decoration Proteins / Ig-like|
|Sample||Marine Phage SIO-2|
|Source||Vibrio phage SIO-2 / virus / SIO-2|
|Map data||SIO-2 prophage|
|Method||single particle (icosahedral) reconstruction, at 15 Å resolution|
|Authors||Lander GC / Baudoux AC / Azam F / Potter CS / Carragher B / Johnson JE|
|Citation||Structure, 2012, 20, 498-503|
|Date||Deposition: Jan 10, 2012 / Header (metadata) release: Jan 12, 2012 / Map release: Jan 12, 2012 / Last update: Mar 14, 2012|
Downloads & links
|File||emd_5383.map.gz (map file in CCP4 format, 22783 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 3.9 Å|
CCP4 map header:
-Entire Marine Phage SIO-2
|Entire||Name: Marine Phage SIO-2 / Details: procapsid / Number of components: 1 / Oligomeric State: immature capsid|
|Mass||Theoretical: 12.2 MDa|
-Component #1: virus, Vibrio phage SIO-2
|Virus||Name: Vibrio phage SIO-2 / a.k.a: SIO-2 / Class: VIRION / Details: particles were present with mature phage prep / Empty: Yes / Enveloped: No / Isolate: STRAIN|
|Mass||Theoretical: 12.2 MDa|
|Species||Species: Vibrio phage SIO-2 / virus / SIO-2|
|Source (natural)||Host Species: Vibrio sp. swat-3 / bacteria / Host category: BACTERIA(EUBACTERIA)|
|Shell #1||Name of element: gene84 / Diameter: 600 Å / T number(triangulation number): 12|
|Sample solution||Buffer solution: 100 kDa-filtered autoclaved seawater|
|Support film||200 mesh Cu grid|
|Vitrification||Instrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 78 K / Humidity: 100 % / Method: blot for 4 seconds before plunging / Details: Vitrification instrument: Vitrobot|
-Electron microscopy imaging
|Imaging||Microscope: FEI TECNAI 20 / Date: Jun 13, 2009 / Details: Collected using Leginon software|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 30 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 80000 X (nominal), 80000 X (calibrated)|
Astigmatism: objective lens astigmatism was corrected at 210K times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1800 - 3000 nm
|Specimen Holder||Holder: Gatan CT3500 / Model: GATAN LIQUID NITROGEN / Temperature: 78 K ( 78 - 78 K)|
|Camera||Detector: TVIPS TEMCAM-F415 (4k x 4k)|
|Image acquisition||Number of digital images: 6628 / Sampling size: 0.975 microns|
|Processing||Method: single particle (icosahedral) reconstruction|
Details: particles automatically selected and manually edited
Number of projections: 1179 / Applied symmetry: I (icosahedral)
|3D reconstruction||Algorithm: Projection matching / Software: EMAN and Frealign / CTF correction: whole micrograph / Resolution: 15 Å / Resolution method: FSC 0.5|
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