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Yorodumi- EMDB-37185: Jackbean Urease (Fourier cropped K3 super resolution then PASR pr... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37185 | |||||||||
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Title | Jackbean Urease (Fourier cropped K3 super resolution then PASR pre-processed) (Original data: EMPIAR-10549) | |||||||||
Map data | Preprocessed map JBU PASR | |||||||||
Sample |
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Keywords | PASR / post-acquisition super resolution / jackbean urase / EMPIAR dataset / HYDROLASE | |||||||||
Biological species | Canavalia ensiformis (jack bean) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.19 Å | |||||||||
Authors | Burton-Smith RN / Murata K | |||||||||
Funding support | Japan, 1 items
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Citation | Journal: To Be Published Title: Jackbean Urease (Fourier cropped K3 super resolution then PASR pre-processed) (Original data: EMPIAR-10549) Authors: Burton-Smith RN / Murata K | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37185.map.gz | 49.4 MB | EMDB map data format | |
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Header (meta data) | emd-37185-v30.xml emd-37185.xml | 11.4 KB 11.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_37185_fsc.xml | 8.5 KB | Display | FSC data file |
Images | emd_37185.png | 119.5 KB | ||
Filedesc metadata | emd-37185.cif.gz | 3.7 KB | ||
Others | emd_37185_half_map_1.map.gz emd_37185_half_map_2.map.gz | 40.7 MB 40.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37185 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37185 | HTTPS FTP |
-Validation report
Summary document | emd_37185_validation.pdf.gz | 922 KB | Display | EMDB validaton report |
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Full document | emd_37185_full_validation.pdf.gz | 921.5 KB | Display | |
Data in XML | emd_37185_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | emd_37185_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37185 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37185 | HTTPS FTP |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_37185.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Preprocessed map JBU PASR | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half-map 1 JBU PASR
File | emd_37185_half_map_1.map | ||||||||||||
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Annotation | Half-map 1 JBU PASR | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map 2 JBU PASR
File | emd_37185_half_map_2.map | ||||||||||||
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Annotation | Half-map 2 JBU PASR | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Jackbean urease
Entire | Name: Jackbean urease |
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Components |
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-Supramolecule #1: Jackbean urease
Supramolecule | Name: Jackbean urease / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Canavalia ensiformis (jack bean) |
Molecular weight | Theoretical: 550 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 39.93 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |