+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3228 | |||||||||
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Title | Sub-tomogram averaging in RELION | |||||||||
Map data | ab-initio reconstruction of the S. cerevisiae 80S ribosome using sub-tomogram averaging in RELION | |||||||||
Sample |
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Keywords | sub-tomogram averaging / RELION / regularized-likelihood / tomography / cryo-EM / ribosome | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 13.0 Å | |||||||||
Authors | Bharat TAM / Scheres SHW | |||||||||
Citation | Journal: To Be Published Title: Sub-tomogram averaging in RELION Authors: Bharat TAM / Scheres SHW | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3228.map.gz | 19.6 MB | EMDB map data format | |
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Header (meta data) | emd-3228-v30.xml emd-3228.xml | 8 KB 8 KB | Display Display | EMDB header |
Images | EMD-3228_ribosome_picture_EMDB.png | 98.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3228 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3228 | HTTPS FTP |
-Validation report
Summary document | emd_3228_validation.pdf.gz | 251.9 KB | Display | EMDB validaton report |
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Full document | emd_3228_full_validation.pdf.gz | 251 KB | Display | |
Data in XML | emd_3228_validation.xml.gz | 5.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3228 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3228 | HTTPS FTP |
-Related structure data
Similar structure data | |
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EM raw data | EMPIAR-10045 (Title: Sub-tomogram averaging in RELION / Data size: 842.8 Data #1: Raw data and also processed datafor sub-tomogram averaging of S. cerevisiae 80S ribosomes [class averages]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_3228.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | ab-initio reconstruction of the S. cerevisiae 80S ribosome using sub-tomogram averaging in RELION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.17 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 : S. cervisiae 80 S ribosome
Entire | Name: S. cervisiae 80 S ribosome |
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Components |
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-Supramolecule #1000: S. cervisiae 80 S ribosome
Supramolecule | Name: S. cervisiae 80 S ribosome / type: sample / ID: 1000 / Oligomeric state: monomer / Number unique components: 1 |
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-Supramolecule #1: S. cerevisiae 80S ribosome
Supramolecule | Name: S. cerevisiae 80S ribosome / type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: Sacharomyces cerevisiae / synonym: Saccharomyces cerevisiae |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Grid | Details: 200 mesh Copper/Rhodium grid R 2/2 from Quantifoil with a extra thin layer of carbon deposited before sample application |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: Gatan Quantum Energy Filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Date | May 24, 2013 |
Image recording | Category: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60 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: 5.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 53000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 ° |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |