+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16440 | ||||||||||||
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Title | C1 reconstruction of Tanay virus particle | ||||||||||||
Map data | C1 reconstruction of TANAV particle | ||||||||||||
Sample |
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Keywords | Mosquito virus / Negevirus / Envelope / VIRUS | ||||||||||||
Biological species | Tanay virus | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 23.6 Å | ||||||||||||
Authors | Okamoto K / Song C / Miyazaki N / Murata K | ||||||||||||
Funding support | Sweden, Japan, 3 items
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Citation | Journal: To Be Published Title: C1 reconstruction of Tanay virus particle Authors: Okamoto K / Song C / Miyazaki N / Murata K | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16440.map.gz | 222.1 MB | EMDB map data format | |
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Header (meta data) | emd-16440-v30.xml emd-16440.xml | 11.4 KB 11.4 KB | Display Display | EMDB header |
Images | emd_16440.png | 56.5 KB | ||
Filedesc metadata | emd-16440.cif.gz | 3.7 KB | ||
Others | emd_16440_half_map_1.map.gz emd_16440_half_map_2.map.gz | 193.6 MB 193.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16440 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16440 | HTTPS FTP |
-Validation report
Summary document | emd_16440_validation.pdf.gz | 858.9 KB | Display | EMDB validaton report |
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Full document | emd_16440_full_validation.pdf.gz | 858.5 KB | Display | |
Data in XML | emd_16440_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | emd_16440_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16440 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16440 | HTTPS FTP |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_16440.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | C1 reconstruction of TANAV particle | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.992 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half-map1
File | emd_16440_half_map_1.map | ||||||||||||
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Annotation | Half-map1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map2
File | emd_16440_half_map_2.map | ||||||||||||
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Annotation | Half-map2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Tanay virus
Entire | Name: Tanay virus |
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Components |
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-Supramolecule #1: Tanay virus
Supramolecule | Name: Tanay virus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 1489714 / Sci species name: Tanay virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
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-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | JEOL 2200FS |
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Image recording | Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Average electron dose: 20.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.5 µm |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 23.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 10282 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |