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Yorodumi- EMDB-25842: 1.85A reconstruction of mouse heavy chain apoferritin collected a... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25842 | |||||||||
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Title | 1.85A reconstruction of mouse heavy chain apoferritin collected at 346 micrographs/hr | |||||||||
Map data | Sharp Map | |||||||||
Sample |
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Keywords | METAL TRANSPORT | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 1.85 Å | |||||||||
Authors | Peck JV / Fay JF / Strauss JD | |||||||||
Funding support | 1 items
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Citation | Journal: IUCrJ / Year: 2022 Title: High-speed high-resolution data collection on a 200 keV cryo-TEM. Authors: Jared V Peck / Jonathan F Fay / Joshua D Strauss / Abstract: Limitations to successful single-particle cryo-electron microscopy (cryo-EM) projects include stable sample generation, production of quality cryo-EM grids with randomly oriented particles embedded ...Limitations to successful single-particle cryo-electron microscopy (cryo-EM) projects include stable sample generation, production of quality cryo-EM grids with randomly oriented particles embedded in thin vitreous ice and access to microscope time. To address the limitation of microscope time, methodologies to more efficiently collect data on a 200 keV Talos Arctica cryo-transmission electron microscope at speeds as fast as 720 movies per hour (∼17 000 per day) were tested. In this study, key parameters were explored to increase data collection speed including: (1) using the beam-image shift method to acquire multiple images per stage position, (2) employing UltrAufoil TEM grids with R0.6/1 hole spacing, (3) collecting hardware-binned data and (4) adjusting the image shift delay factor in . Here, eight EM maps of mouse apoferritin at 1.8-1.9 Å resolution were obtained in the analysis with data collection times for each dataset ranging from 56 min to 2 h. An EM map of mouse apoferritin at 1.78 Å was obtained from an overnight data collection at a speed of 500 movies per hour and subgroup analysis performed, with no significant variation observed in data quality by image shift distance and image shift delay. The findings and operating procedures detailed herein allow for rapid turnover of single-particle cryo-EM structure determination. | |||||||||
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_25842.map.gz | 778.2 MB | EMDB map data format | |
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Header (meta data) | emd-25842-v30.xml emd-25842.xml | 11.6 KB 11.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_25842_fsc.xml | 20.8 KB | Display | FSC data file |
Images | emd_25842.png | 95.6 KB | ||
Filedesc metadata | emd-25842.cif.gz | 3.7 KB | ||
Others | emd_25842_half_map_1.map.gz emd_25842_half_map_2.map.gz | 763.2 MB 763.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25842 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25842 | HTTPS FTP |
-Validation report
Summary document | emd_25842_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_25842_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_25842_validation.xml.gz | 29.4 KB | Display | |
Data in CIF | emd_25842_validation.cif.gz | 38.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25842 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25842 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_25842.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sharp Map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.44 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: Unfiltered half map A
File | emd_25842_half_map_1.map | ||||||||||||
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Annotation | Unfiltered half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered half map B
File | emd_25842_half_map_2.map | ||||||||||||
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Annotation | Unfiltered half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : mouse heavy chain apoferritin
Entire | Name: mouse heavy chain apoferritin |
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Components |
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-Supramolecule #1: mouse heavy chain apoferritin
Supramolecule | Name: mouse heavy chain apoferritin / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 487.32 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 95 % |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 54.3 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.59 µm / Nominal defocus min: 0.46 µm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |