+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9203 | |||||||||
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Title | bovine glutamate dehydrogenase (18apr21a) | |||||||||
Map data | bovine glutamate dehydrogenase map (18apr21a) | |||||||||
Sample |
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Biological species | Bos taurus (cattle) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.1 Å | |||||||||
Authors | Eng ET / Kopylov M / Negro CJ / Dallaykan S / Jordan KJ / Kelley K / Rice WJ / Carragher BO / Potter CS | |||||||||
Citation | Journal: J Struct Biol / Year: 2019 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9203.map.gz | 16.6 MB | EMDB map data format | |
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Header (meta data) | emd-9203-v30.xml emd-9203.xml | 19.6 KB 19.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_9203_fsc.xml | 12.4 KB | Display | FSC data file |
Images | emd_9203.png | 191.3 KB | ||
Masks | emd_9203_msk_1.map | 166.4 MB | Mask map | |
Others | emd_9203_additional.map.gz emd_9203_half_map_1.map.gz emd_9203_half_map_2.map.gz | 128.9 MB 130.6 MB 130.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9203 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9203 | HTTPS FTP |
-Validation report
Summary document | emd_9203_validation.pdf.gz | 78 KB | Display | EMDB validaton report |
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Full document | emd_9203_full_validation.pdf.gz | 77.1 KB | Display | |
Data in XML | emd_9203_validation.xml.gz | 491 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9203 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9203 | HTTPS FTP |
-Related structure data
Related structure data | 9233C C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10217 (Title: bovine liver glutamate dehydrogenase / Data size: 264.5 Data #1: aligned micrographs of bovine liver glutamate dehydrogenase (18apr21a) [micrographs - single frame]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_9203.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | bovine glutamate dehydrogenase map (18apr21a) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 | emd_9203_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: unsharpened map
File | emd_9203_additional.map | ||||||||||||
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Annotation | unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: odd half map
File | emd_9203_half_map_1.map | ||||||||||||
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Annotation | odd half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: even half map
File | emd_9203_half_map_2.map | ||||||||||||
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Annotation | even half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : bovine liver glutamate dehydrogenase
Entire | Name: bovine liver glutamate dehydrogenase |
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Components |
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-Supramolecule #1: bovine liver glutamate dehydrogenase
Supramolecule | Name: bovine liver glutamate dehydrogenase / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Bos taurus (cattle) |
Molecular weight | Theoretical: 347 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4 mg/mL | |||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 400 / 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 s after a 30 s wait time. | |||||||||
Details | This sample was monodisperse. |
-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: 1-60 / Number grids imaged: 1 / Number real images: 2491 / Average exposure time: 10.2083 sec. / Average electron dose: 61.25 e/Å2 Details: Images were collected in movie mode at 10 frames per second. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
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 |