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Yorodumi- EMDB-40602: cryoEM map for design HE0537, a D4 symmetric homo-oligomer design... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40602 | ||||||||||||
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Title | cryoEM map for design HE0537, a D4 symmetric homo-oligomer designed with RFdiffusion. | ||||||||||||
Map data | Refined cryoEM map for design HE0537 | ||||||||||||
Sample |
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Keywords | De novo / computationally designed / Dihedral / diffusion model / RFdiffusion / BIOSYNTHETIC PROTEIN | ||||||||||||
Biological species | synthetic construct (others) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.06 Å | ||||||||||||
Authors | Courbet A / Baker D / Watson J / Juergens D / Eisenach E | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: To Be Published Title: Broadly applicable protein design with RoseTTAFold Diffusion Authors: Juergens D / Watson J / Eisenach HE / Courbet A | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40602.map.gz | 56.5 MB | EMDB map data format | |
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Header (meta data) | emd-40602-v30.xml emd-40602.xml | 13.3 KB 13.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_40602_fsc.xml | 8.5 KB | Display | FSC data file |
Images | emd_40602.png | 21.4 KB | ||
Masks | emd_40602_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-40602.cif.gz | 4 KB | ||
Others | emd_40602_half_map_1.map.gz emd_40602_half_map_2.map.gz | 59.3 MB 59.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40602 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40602 | HTTPS FTP |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_40602.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Refined cryoEM map for design HE0537 | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.883 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_40602_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half map A of cryoEM map for design HE0537
File | emd_40602_half_map_1.map | ||||||||||||
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Annotation | Half map A of cryoEM map for design HE0537 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B of cryoEM map for design HE0537
File | emd_40602_half_map_2.map | ||||||||||||
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Annotation | Half map B of cryoEM map for design HE0537 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : HE0537
Entire | Name: HE0537 |
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Components |
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-Supramolecule #1: HE0537
Supramolecule | Name: HE0537 / type: complex / ID: 1 / Parent: 0 Details: De novo D4 symmetric homooligomer designed with RFdiffusion |
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Source (natural) | Organism: synthetic construct (others) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 10 mg/mL | |||||||||
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Buffer | pH: 8.4 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | TFS GLACIOS |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 1116 / Average electron dose: 50.0 e/Å2 |