|Entry||Database: EMDB / ID: 5142|
|Title||Ab initio reconstruction of the avian polyomavirus via the asymmetric random-model method|
|Map data||The avian polyomavirus|
|Keywords||random-model method / ab initio reconstruction / avian polyomavirus|
|Source||Avian polyomavirus (Avian polyomavirus)|
|Method||single particle reconstruction / cryo EM / 35 Å resolution|
|Authors||Sanz E / Stewart AB / Belnap DM|
|Citation||Journal: J. Struct. Biol. / Year: 2010|
Title: The random-model method enables ab initio 3D reconstruction of asymmetric particles and determination of particle symmetry.
Authors: Eduardo Sanz-García / Aaron B Stewart / David M Belnap
Abstract: Model-based, 3D reconstruction techniques depend on reliable starting models. We present an extension of the random-model method (RMM) that allows the ab initio generation of suitable starting models ...Model-based, 3D reconstruction techniques depend on reliable starting models. We present an extension of the random-model method (RMM) that allows the ab initio generation of suitable starting models directly from un-averaged, experimental images of asymmetric or symmetric particles. Therefore, the asymmetric RMM can also be used to determine point-group symmetry. The procedure is facilitated by the use of (a) variable angular step-sizes during iterative origin and orientation searches, (b) high numbers of particle images, and (c) highly defocused images. The method is inhibited by mixed-handedness orientation assignments and by particles with inconspicuous features. For symmetric particles, symmetric RMMs can overcome these deficiencies.
|Date||Deposition: Nov 21, 2009 / Header (metadata) release: Apr 26, 2010 / Map release: Apr 26, 2010 / Last update: Jun 21, 2010|
|Structure viewer||EM map: |
Downloads & links
|File||emd_5142.map.gz (map file in CCP4 format, 193091 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.63 Å|
CCP4 map header:
-Entire Avian polyomavirus
|Entire||Name: Avian polyomavirus / Number of components: 1|
-Component #1: virus, Avian polyomavirus
|Virus||Name: Avian polyomavirus / a.k.a: Avian polyomavirus / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN|
|Species||Species: Avian polyomavirus (Avian polyomavirus)|
|Source (natural)||Host Species: Aves / Host category: VERTEBRATES|
|Shell #1||Name of element: VP1 / Diameter: 520 Å / T number(triangulation number): 7|
|Specimen||Specimen state: particle / Method: cryo EM|
|Vitrification||Instrument: FEI VITROBOT / Cryogen name: ETHANE / Details: Vitrification instrument: Vitrobot|
-Electron microscopy imaging
Model: Tecnai F30 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F30|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 39000 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 700 - 4900 nm|
|Specimen Holder||Holder: Eucentric / Model: GATAN LIQUID NITROGEN|
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 6.3 microns|
|Processing||Method: single particle reconstruction / Number of projections: 4198 / Applied symmetry: C1 (asymmetric)|
|3D reconstruction||Algorithm: Projection matching / Software: PFT3DR, Bsoft / CTF correction: None|
Details: Random-model method. Angular step-size was initially set to 20 deg. in the first iteration and gradually decreased by 0.19 deg. in each successive iteration, until a lower limit of 1 deg. was reached.
Resolution: 35 Å / Resolution method: FSC 0.5
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