+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28761 | |||||||||
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Title | Mycobacterium phage Che8 mutant capsid (gene 110 deletion) | |||||||||
Map data | Sharpened map of Che_mutant_map.mrc. | |||||||||
Sample |
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Keywords | HK97-fold / T=9 / tailed bacteriophage / VIRUS | |||||||||
Biological species | Mycobacterium phage Che8 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.39 Å | |||||||||
Authors | Podgorski JM / White SJ | |||||||||
Funding support | 1 items
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Citation | Journal: To Be Published Title: Diverse O-linked Glycosylation of phage structural proteins is mediated through phage-encoded glycosyltransferases. Authors: Pope WH / Hatfull GF | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28761.map.gz | 1.5 GB | EMDB map data format | |
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Header (meta data) | emd-28761-v30.xml emd-28761.xml | 16.6 KB 16.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28761_fsc.xml | 26.2 KB | Display | FSC data file |
Images | emd_28761.png | 316.3 KB | ||
Masks | emd_28761_msk_1.map | 1.9 GB | Mask map | |
Filedesc metadata | emd-28761.cif.gz | 4.2 KB | ||
Others | emd_28761_additional_1.map.gz emd_28761_half_map_1.map.gz emd_28761_half_map_2.map.gz | 1.8 GB 1.8 GB 1.8 GB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28761 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28761 | HTTPS FTP |
-Validation report
Summary document | emd_28761_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_28761_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_28761_validation.xml.gz | 36.4 KB | Display | |
Data in CIF | emd_28761_validation.cif.gz | 48.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28761 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28761 | HTTPS FTP |
-Related structure data
Related structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_28761.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Sharpened map of Che_mutant_map.mrc. | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.182 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_28761_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Ewald sphere corrected map.
File | emd_28761_additional_1.map | ||||||||||||
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Annotation | Ewald sphere corrected map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map of ewald sphere corrected Che mutant map.mrc.
File | emd_28761_half_map_1.map | ||||||||||||
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Annotation | Half map of ewald sphere corrected Che_mutant_map.mrc. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map of ewald sphere corrected Che mutant map.mrc.
File | emd_28761_half_map_2.map | ||||||||||||
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Annotation | Half map of ewald sphere corrected Che_mutant_map.mrc. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Mycobacterium phage Che8
Entire | Name: Mycobacterium phage Che8 (virus) |
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Components |
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-Supramolecule #1: Mycobacterium phage Che8
Supramolecule | Name: Mycobacterium phage Che8 / type: virus / ID: 1 / Parent: 0 / Details: MUTANT. Gene 110 deleted. / NCBI-ID: 2907829 / Sci species name: Mycobacterium phage Che8 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) |
Virus shell | Shell ID: 1 / Diameter: 730.0 Å / T number (triangulation number): 9 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 10 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 8118 / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |