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Yorodumi- EMDB-18232: CryoDRGN Reconstruction of 80S Ribosome in Unrotated State from S... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18232 | |||||||||
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Title | CryoDRGN Reconstruction of 80S Ribosome in Unrotated State from S.cerevisiae Prepared using Cryo-plasmaFIB Milling | |||||||||
Map data | TOMOMAN-STOPGAP-Warp-Relion-M CryoDRGN-ET 80S yeast unrotated | |||||||||
Sample |
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Keywords | yeast 80S / RIBOSOME | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 4.5 Å | |||||||||
Authors | Rangan R / Khavnekar S / Lerer A / Johnston J / Kelley R / Obr M / Kotecha A / Zhong ED | |||||||||
Funding support | Germany, 2 items
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Citation | Journal: To Be Published Title: Deep reconstructing generative networks for visualizing dynamic biomolecules inside cells Authors: Rangan R / Khavnekar S / Lerer A / Johnston J / Kelley R / Obr M / Kotecha A / Zhong ED | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_18232.map.gz | 59.4 MB | EMDB map data format | |
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Header (meta data) | emd-18232-v30.xml emd-18232.xml | 12.7 KB 12.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_18232_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_18232.png | 81.3 KB | ||
Masks | emd_18232_msk_1.map | 64 MB | Mask map | |
Others | emd_18232_half_map_1.map.gz emd_18232_half_map_2.map.gz | 59.3 MB 59.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18232 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18232 | HTTPS FTP |
-Validation report
Summary document | emd_18232_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_18232_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_18232_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | emd_18232_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18232 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18232 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_18232.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | TOMOMAN-STOPGAP-Warp-Relion-M CryoDRGN-ET 80S yeast unrotated | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.96 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_18232_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: TOMOMAN-STOPGAP-Warp-Relion-M CryoDRGN-ET 80S yeast unrotated
File | emd_18232_half_map_1.map | ||||||||||||
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Annotation | TOMOMAN-STOPGAP-Warp-Relion-M CryoDRGN-ET 80S yeast unrotated | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: TOMOMAN-STOPGAP-Warp-Relion-M CryoDRGN-ET 80S yeast unrotated
File | emd_18232_half_map_2.map | ||||||||||||
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Annotation | TOMOMAN-STOPGAP-Warp-Relion-M CryoDRGN-ET 80S yeast unrotated | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : 80S S. cerevisiae
Entire | Name: 80S S. cerevisiae |
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Components |
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-Supramolecule #1: 80S S. cerevisiae
Supramolecule | Name: 80S S. cerevisiae / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 3.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |