+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33163 | |||||||||
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Title | 3D structure of the base in oval-shaped WSSV capsids | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Complex / C14 / capsid / base / VIRAL PROTEIN | |||||||||
Biological species | White spot syndrome virus | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 5.88 Å | |||||||||
Authors | Shan H / Liu MD / Shen QT | |||||||||
Funding support | China, 1 items
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Citation | Journal: To Be Published Title: 3D structure of the base in oval-shaped WSSV capsids Authors: Shan H / Liu MD / Shen QT | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33163.map.gz | 118.3 MB | EMDB map data format | |
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Header (meta data) | emd-33163-v30.xml emd-33163.xml | 11.3 KB 11.3 KB | Display Display | EMDB header |
Images | emd_33163.png | 184.8 KB | ||
Filedesc metadata | emd-33163.cif.gz | 3.5 KB | ||
Others | emd_33163_half_map_1.map.gz emd_33163_half_map_2.map.gz | 226 MB 226 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33163 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33163 | HTTPS FTP |
-Validation report
Summary document | emd_33163_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_33163_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_33163_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | emd_33163_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33163 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33163 | HTTPS FTP |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_33163.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.01 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_33163_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33163_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : wssv
Entire | Name: wssv |
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Components |
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-Supramolecule #1: wssv
Supramolecule | Name: wssv / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: White spot syndrome virus |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Staining | Type: NEGATIVE / Material: uranyl acetate |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.25 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 5.88 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1683 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |