+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20156 | |||||||||
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Title | Apoferritin from equine spleen at 3.9 AngstromFerritin | |||||||||
Map data | Sharpen map | |||||||||
Sample |
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Function / homology | Function and homology information intracellular ferritin complex / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / iron ion transport / iron ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Equus caballus (horse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Mendez JH / Randolph P / Stagg SM | |||||||||
Funding support | United States, 1 items
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Citation | Journal: IUCrJ / Year: 2019 Title: Throughput and resolution with a next-generation direct electron detector. Authors: Joshua H Mendez / Atousa Mehrani / Peter Randolph / Scott Stagg / Abstract: Direct electron detectors (DEDs) have revolutionized cryo-electron microscopy (cryo-EM) by facilitating the correction of beam-induced motion and radiation damage, and also by providing high- ...Direct electron detectors (DEDs) have revolutionized cryo-electron microscopy (cryo-EM) by facilitating the correction of beam-induced motion and radiation damage, and also by providing high-resolution image capture. A new-generation DED, the DE64, has been developed by Direct Electron that has good performance in both integrating and counting modes. The camera has been characterized in both modes in terms of image quality, throughput and resolution of cryo-EM reconstructions. The modulation transfer function, noise power spectrum and detective quantum efficiency (DQE) were determined for both modes, as well as the number of images per unit time. Although the DQE for counting mode was superior to that for integrating mode, the data-collection throughput for this mode was more than ten times slower. Since throughput and resolution are related in single-particle cryo-EM, data for apoferritin were collected and reconstructed using integrating mode, integrating mode in conjunction with a Volta phase plate (VPP) and counting mode. Only the counting-mode data resulted in a better than 3 Å resolution reconstruction with similar numbers of particles, and this increased performance could not be compensated for by the increased throughput of integrating mode or by the increased low-frequency contrast of integrating mode with the VPP. These data show that the superior image quality provided by counting mode is more important for high-resolution cryo-EM reconstructions than the superior throughput of integrating mode. | |||||||||
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_20156.map.gz | 8.4 MB | EMDB map data format | |
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Header (meta data) | emd-20156-v30.xml emd-20156.xml | 14.8 KB 14.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_20156_fsc.xml | 7.9 KB | Display | FSC data file |
Images | emd_20156.png | 122.8 KB | ||
Others | emd_20156_half_map_1.map.gz emd_20156_half_map_2.map.gz | 29.6 MB 29.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20156 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20156 | 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_20156.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sharpen map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.973 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: Even half map
File | emd_20156_half_map_1.map | ||||||||||||
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Annotation | Even half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Odd half map
File | emd_20156_half_map_2.map | ||||||||||||
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Annotation | Odd half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Apoferritin from equine spleen.
Entire | Name: Apoferritin from equine spleen.Ferritin |
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Components |
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-Supramolecule #1: Apoferritin from equine spleen.
Supramolecule | Name: Apoferritin from equine spleen. / type: complex / ID: 1 / Parent: 0 / Details: Apoferritin readily available from Sigma-Aldrich. |
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Source (natural) | Organism: Equus caballus (horse) / Tissue: Spleen |
Molecular weight | Theoretical: 481 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: NITROGEN |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: DIRECT ELECTRON DE-64 (8k x 8k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 8192 pixel / Digitization - Dimensions - Height: 8192 pixel / Digitization - Sampling interval: 6.5 µm / Digitization - Frames/image: 1-42 / Number grids imaged: 1 / Number real images: 109 / Average exposure time: 1.3 sec. / Average electron dose: 61.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |