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Yorodumi- EMDB-9260: Electron cryotomogram of Bdellovibrio bacteriovorus acquired by f... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9260 | |||||||||
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Title | Electron cryotomogram of Bdellovibrio bacteriovorus acquired by fast-incremental method | |||||||||
Map data | Tomographic reconstruction of Bdellovibrio cell. Binned 4 times. | |||||||||
Sample |
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Biological species | Bdellovibrio bacteriovorus (bacteria) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Chreifi G / Chen S / Metskas LA / Kaplan M / Jensen GJ | |||||||||
Citation | Journal: J Struct Biol / Year: 2019 Title: Rapid tilt-series acquisition for electron cryotomography. Authors: Georges Chreifi / Songye Chen / Lauren Ann Metskas / Mohammed Kaplan / Grant J Jensen / Abstract: Using a new Titan Krios stage equipped with a single-axis holder, we developed two methods to accelerate the collection of tilt-series. We demonstrate a continuous-tilting method that can record a ...Using a new Titan Krios stage equipped with a single-axis holder, we developed two methods to accelerate the collection of tilt-series. We demonstrate a continuous-tilting method that can record a tilt-series in seconds, but with loss of details finer than ∼4 nm. We also demonstrate a fast-incremental method that can record a tilt-series several-fold faster than current methods and with similar resolution. We characterize the utility of both methods in real biological electron cryotomography workflows. We identify opportunities for further improvements in hardware and software and speculate on the impact such advances could have on structural biology. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9260.map.gz | 865.8 MB | EMDB map data format | |
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Header (meta data) | emd-9260-v30.xml emd-9260.xml | 8.8 KB 8.8 KB | Display Display | EMDB header |
Images | emd_9260.png | 138.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9260 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9260 | HTTPS FTP |
-Validation report
Summary document | emd_9260_validation.pdf.gz | 78.9 KB | Display | EMDB validaton report |
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Full document | emd_9260_full_validation.pdf.gz | 78 KB | Display | |
Data in XML | emd_9260_validation.xml.gz | 499 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9260 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9260 | HTTPS FTP |
-Related structure data
Related structure data | 9261C C: citing same article (ref.) |
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EM raw data | EMPIAR-10226 (Title: Bdellovibrio bacteriovorus electron cryotomography tilt-series acquired by fast-incremental method Data size: 5.2 Data #1: Bdellovibrio bacteriovorus electron cryotomography tilt-series acquired by fast-incremental method [tilt series]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_9260.map.gz / Format: CCP4 / Size: 1017.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Tomographic reconstruction of Bdellovibrio cell. Binned 4 times. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 10.97 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Bdellovibrio bacteriovorus
Entire | Name: Bdellovibrio bacteriovorus (bacteria) |
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Components |
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-Supramolecule #1: Bdellovibrio bacteriovorus
Supramolecule | Name: Bdellovibrio bacteriovorus / type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Bdellovibrio bacteriovorus (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.8 |
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Grid | Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12.0 nm / Details: unspecified |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 296 K / Instrument: FEI VITROBOT MARK IV |
Sectioning | Other: NO SECTIONING |
Fiducial marker | Manufacturer: Ted Pella / Diameter: 10 nm |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: SIMULTANEOUS ITERATIVE (SIRT) / Software - Name: TOMO3D (ver. 2.0) / Number images used: 95 |
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CTF correction | Software - Name: IMOD (ver. 4.10.18) / Software - details: ctfplotter was used to estimate defocus |