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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-9233 | |||||||||
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Title | T20S proteasome | |||||||||
![]() | T20S sharpened masked map | |||||||||
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Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.1 Å | |||||||||
![]() | Eng ET / Kopylov M / Jordan KJ / Rice WJ / Carragher BO / Potter CS | |||||||||
![]() | ![]() Title: Reducing cryoEM file storage using lossy image formats. Authors: Edward T Eng / Mykhailo Kopylov / Carl J Negro / Sarkis Dallaykan / William J Rice / Kelsey D Jordan / Kotaro Kelley / Bridget Carragher / Clinton S Potter / ![]() Abstract: Recent advances in instrumentation and software for cryoEM have increased the applicability and utility of this method. High levels of automation and faster data acquisition rates require hard ...Recent advances in instrumentation and software for cryoEM have increased the applicability and utility of this method. High levels of automation and faster data acquisition rates require hard decisions to be made regarding data retention. Here we investigate the efficacy of data compression applied to aligned summed movie files. Surprisingly, these images can be compressed using a standard lossy method that reduces file storage by 90-95% and yet can still be processed to provide sub-2 Å reconstructed maps. We do not advocate this as an archival method, but it may provide a useful means for retaining images as an historical record, especially at large facilities. | |||||||||
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 | ![]() | 30.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.8 KB 19.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.1 KB | Display | ![]() |
Images | ![]() | 217.7 KB | ||
Masks | ![]() | 244.1 MB | ![]() | |
Others | ![]() ![]() ![]() | 192.9 MB 194 MB 194.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9203C C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data #1: unaligned multi-frame micrographs of T20S (18mar31a) [micrographs - multiframe]) |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | T20S sharpened masked map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.6616 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | ![]() | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: T20S unsharpened map
File | emd_9233_additional.map | ||||||||||||
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Annotation | T20S unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: T20S even half map
File | emd_9233_half_map_1.map | ||||||||||||
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Annotation | T20S even half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: T20S odd half map
File | emd_9233_half_map_2.map | ||||||||||||
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Annotation | T20S odd half map | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : 20S proteasome
Entire | Name: 20S proteasome |
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Components |
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-Supramolecule #1: 20S proteasome
Supramolecule | Name: 20S proteasome / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
Molecular weight | Theoretical: 700 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.21 mg/mL | |||||||||
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Buffer | pH: 7.4 Component:
Details: 20 mM Tris, 150 mM NaCl | |||||||||
Grid | Model: C-flat-1.2/1.3 4C / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 75 % / Chamber temperature: 298 K / Instrument: GATAN CRYOPLUNGE 3 Details: Blotted for 2.5 seconds after a 30 second wait time.. | |||||||||
Details | 1.2/1.3 C-Flat grid, plasma cleaned |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 70.0 K / Max: 70.0 K |
Details | Leginon |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-50 / Number grids imaged: 1 / Number real images: 1173 / Average exposure time: 6.259 sec. / Average electron dose: 62.59 e/Å2 Details: Images were collected in movie mode at 5 frames per second. |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.02 µm / Calibrated defocus min: 0.2 µm / Calibrated magnification: 75574 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 37000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |