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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-6398 | |||||||||
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Title | Electron cryo-microscopy of a Propionibacterium acnes phage | |||||||||
![]() | Reconstruction of Propionibacterium acnes phage | |||||||||
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![]() | acne / bacteriophage / cryoEM / HK97-like | |||||||||
Function / homology | Gp6![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
![]() | Chiou J / Zhang X / Marinelli LJ / Modlin RL / Zhou ZH | |||||||||
![]() | ![]() Title: Capsid Structure of the Propionibacterium acnes Bacteriophage ATCC_Clear Authors: Chiou J / Zhang X / Marinelli LJ / Modlin RL / Zhou ZH | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 466 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 8.9 KB 8.9 KB | Display Display | ![]() |
Images | ![]() | 205.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 379.7 KB | Display | ![]() |
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Full document | ![]() | 379.3 KB | Display | |
Data in XML | ![]() | 7.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3jb5MC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of Propionibacterium acnes phage | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Propionibacterium acnes bacteriophage ATCC_Clear capsid structure
Entire | Name: Propionibacterium acnes bacteriophage ATCC_Clear capsid structure |
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Components |
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-Supramolecule #1000: Propionibacterium acnes bacteriophage ATCC_Clear capsid structure
Supramolecule | Name: Propionibacterium acnes bacteriophage ATCC_Clear capsid structure type: sample / ID: 1000 / Number unique components: 1 |
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Molecular weight | Experimental: 33 MDa / Method: SDS-PAGE/MS |
-Supramolecule #1: Propionibacterium phage PA6
Supramolecule | Name: Propionibacterium phage PA6 / type: virus / ID: 1 / Name.synonym: Propionibacterium acnes bacteriophage / Details: Mature virions, DNA inside masked / NCBI-ID: 376758 / Sci species name: Propionibacterium phage PA6 / Sci species strain: ATCC 29399B_C / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: Propionibacterium acnes bacteriophage |
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Host (natural) | Organism: ![]() |
Virus shell | Shell ID: 1 / Diameter: 660 Å / T number (triangulation number): 7 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Grid | Details: Purified sample was applied to a Quantifoil grid |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Method: Blot for 15 seconds before plunging |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Date | May 16, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 3168 / Average electron dose: 25 e/Å2 Details: Every image is the average of twelve frames recorded by the direct electron detector. |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 38462 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.27 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 38462 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Details | The particles were selected using an in-house selection procedure. |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: OTHER / Software - Name: FREALIGN / Number images used: 27504 |