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Yorodumi- EMDB-29939: EM map of de novo designed protein nanopore RNR_C6_3 using a rein... -
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Open data
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Basic information
| Entry | ![]() | ||||||||||||
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| Title | EM map of de novo designed protein nanopore RNR_C6_3 using a reinforcement learning approach | ||||||||||||
Map data | EM map of de novo designed protein nanopore RNR_C6_3 | ||||||||||||
Sample |
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Keywords | De novo / computationally designed / nanopore / deep learning / BIOSYNTHETIC PROTEIN | ||||||||||||
| Biological species | synthetic construct (others) | ||||||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 5.13 Å | ||||||||||||
Authors | Courbet A / Baker D | ||||||||||||
| Funding support | United States, 3 items
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Citation | Journal: To be publishedTitle: Top-down design of protein architectures with reinforcement learning Authors: Courbet A / Lutz I | ||||||||||||
| History |
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Structure visualization
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_29939.map.gz | 96.9 MB | EMDB map data format | |
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| Header (meta data) | emd-29939-v30.xml emd-29939.xml | 12.7 KB 12.7 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_29939_fsc.xml | 9.9 KB | Display | FSC data file |
| Images | emd_29939.png | 40.1 KB | ||
| Filedesc metadata | emd-29939.cif.gz | 3.8 KB | ||
| Others | emd_29939_half_map_1.map.gz emd_29939_half_map_2.map.gz | 95.4 MB 95.4 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29939 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29939 | HTTPS FTP |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Map
| File | Download / File: emd_29939.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | EM map of de novo designed protein nanopore RNR_C6_3 | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| 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
-Half map: EM half map A of de novo designed protein nanopore RNR C6 3
| File | emd_29939_half_map_1.map | ||||||||||||
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| Annotation | EM half map A of de novo designed protein nanopore RNR_C6_3 | ||||||||||||
| Projections & Slices |
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| Density Histograms |
-Half map: EM half map B of de novo designed protein nanopore RNR C6 3
| File | emd_29939_half_map_2.map | ||||||||||||
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| Annotation | EM half map B of de novo designed protein nanopore RNR_C6_3 | ||||||||||||
| Projections & Slices |
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| Density Histograms |
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Sample components
-Entire : strut_C6_21
| Entire | Name: strut_C6_21 |
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| Components |
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-Supramolecule #1: strut_C6_21
| Supramolecule | Name: strut_C6_21 / type: complex / ID: 1 / Parent: 0 |
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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 |
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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 |
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Electron microscopy
| Microscope | TFS GLACIOS |
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| 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 |
| Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
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About Yorodumi



Keywords
Authors
United States, 3 items
Citation
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Y (Row.)
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Processing
FIELD EMISSION GUN
