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- EMDB-1557: Cryo-EM density map of Epsilon-15 bacteriophage icosahedral recon... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-1557 | |||||||||
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Title | Cryo-EM density map of Epsilon-15 bacteriophage icosahedral reconstruction from JADAS automatically acquired data at 7.3 Angstrom resolution. | |||||||||
![]() | This is the density map of the epsilon-15 bacteriophage reconstructed from JADAS automatically acquired images. | |||||||||
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![]() | Single-particle / Automated data collection / Reconstruction / Cryo-EM / Epsilon-15 bacteriophage | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.3 Å | |||||||||
![]() | Zhang J / Nakamura N / Shimizu Y / Liang N / Liu X / Jakana J / Marsh MP / Booth CR / Shinkawa T / Nakata M / Chiu W | |||||||||
![]() | ![]() Title: JADAS: a customizable automated data acquisition system and its application to ice-embedded single particles. Authors: Junjie Zhang / Natsuko Nakamura / Yuko Shimizu / Nathan Liang / Xiangan Liu / Joanita Jakana / Michael P Marsh / Christopher R Booth / Takao Shinkawa / Munetaka Nakata / Wah Chiu / ![]() Abstract: The JEOL Automated Data Acquisition System (JADAS) is a software system built for the latest generation of the JEOL Transmission Electron Microscopes. It is designed to partially or fully automate ...The JEOL Automated Data Acquisition System (JADAS) is a software system built for the latest generation of the JEOL Transmission Electron Microscopes. It is designed to partially or fully automate image acquisition for ice-embedded single particles under low dose conditions. Its built-in flexibility permits users to customize the order of various imaging operations. In this paper, we describe how JADAS is used to accurately locate and image suitable specimen areas on a grid of ice-embedded particles. We also demonstrate the utility of JADAS by imaging the epsilon 15 bacteriophage with the JEM3200FSC electron cryo-microscope, showing that sufficient images can be collected in a single 8h session to yield a subnanometer resolution structure which agrees with the previously determined structure. | |||||||||
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 | ![]() | 38.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 9.4 KB 9.4 KB | Display Display | ![]() |
Images | ![]() | 282.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 262.4 KB | Display | ![]() |
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Full document | ![]() | 261.5 KB | Display | |
Data in XML | ![]() | 7.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is the density map of the epsilon-15 bacteriophage reconstructed from JADAS automatically acquired images. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.62 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 : Epsilon-15 bacteriophage
Entire | Name: Epsilon-15 bacteriophage |
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Components |
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-Supramolecule #1000: Epsilon-15 bacteriophage
Supramolecule | Name: Epsilon-15 bacteriophage / type: sample / ID: 1000 Details: The sample is frozen on carbon support film in vitreous ice. Number unique components: 1 |
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Molecular weight | Experimental: 22 MDa / Theoretical: 22 MDa |
-Supramolecule #1: Salmonella phage epsilon15
Supramolecule | Name: Salmonella phage epsilon15 / type: virus / ID: 1 / Name.synonym: Epsilon-15 bacteriophage Details: The sample is frozen on carbon support film in vitreous ice. NCBI-ID: 215158 / Sci species name: Salmonella phage epsilon15 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: Epsilon-15 bacteriophage |
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Host (natural) | Organism: ![]() |
Molecular weight | Experimental: 22 MDa / Theoretical: 22 MDa |
Virus shell | Shell ID: 1 / 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: 400 mesh copper grid with holy carbon film |
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Vitrification | Cryogen name: ETHANE / Instrument: OTHER |
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Electron microscopy
Microscope | JEOL 3200FSC |
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Temperature | Average: 100 K |
Specialist optics | Energy filter - Name: JEOL in-column omega filter |
Details | Data is automatically collected using JEOL Automated Data Acquisition System (JADAS). Microscope used JEM3200FSC |
Image recording | Category: CCD / Film or detector model: GENERIC GATAN (4k x 4k) / Digitization - Sampling interval: 2.62 µm / Number real images: 181 / Average electron dose: 20 e/Å2 / Bits/pixel: 8 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 56680 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal magnification: 40000 |
Sample stage | Specimen holder: JEM3200FSC cryoholder / Specimen holder model: OTHER |
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Image processing
CTF correction | Details: Each CCD image |
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Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.3 Å / Resolution method: OTHER / Software - Name: Multi-path simulated annealing / Number images used: 7543 |