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Yorodumi- EMDB-41917: CryoEM structure of PP7 virus-like particle from a multi-species ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41917 | |||||||||
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Title | CryoEM structure of PP7 virus-like particle from a multi-species dataset | |||||||||
Map data | Final sharpened map | |||||||||
Sample |
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Keywords | PP7 VLP / icosahedral cage / multi-species / VIRUS LIKE PARTICLE | |||||||||
Biological species | Pseudomonas phage PP7 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.36 Å | |||||||||
Authors | Kopylov M / Bobe D / Eng ET | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: CryoEM structure of PP7 virus-like particle from a multi-species dataset Authors: Kopylov M / Bobe D / Eng ET | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41917.map.gz | 398.8 MB | EMDB map data format | |
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Header (meta data) | emd-41917-v30.xml emd-41917.xml | 12.3 KB 12.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41917_fsc.xml | 15.8 KB | Display | FSC data file |
Images | emd_41917.png | 183.4 KB | ||
Masks | emd_41917_msk_1.map | 421.9 MB | Mask map | |
Filedesc metadata | emd-41917.cif.gz | 3.8 KB | ||
Others | emd_41917_half_map_1.map.gz emd_41917_half_map_2.map.gz | 392.1 MB 392.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41917 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41917 | HTTPS FTP |
-Validation report
Summary document | emd_41917_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_41917_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_41917_validation.xml.gz | 25.7 KB | Display | |
Data in CIF | emd_41917_validation.cif.gz | 33.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41917 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41917 | HTTPS FTP |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_41917.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Final sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.096 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_41917_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half B
File | emd_41917_half_map_1.map | ||||||||||||
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Annotation | Half B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half A
File | emd_41917_half_map_2.map | ||||||||||||
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Annotation | Half A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Pseudomonas phage PP7
Entire | Name: Pseudomonas phage PP7 (virus) |
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Components |
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-Supramolecule #1: Pseudomonas phage PP7
Supramolecule | Name: Pseudomonas phage PP7 / type: virus / ID: 1 / Parent: 0 / Details: Virus-like particles / NCBI-ID: 12023 / Sci species name: Pseudomonas phage PP7 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes |
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Molecular weight | Theoretical: 2.5 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 70.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |