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Yorodumi- EMDB-22025: Reprocessing of EMPIAR-10204 data (beta-galactosidase) with parti... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22025 | |||||||||
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Title | Reprocessing of EMPIAR-10204 data (beta-galactosidase) with particles picked by Kpicker | |||||||||
Map data | beta-galactosidase | |||||||||
Sample |
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Function / homology | Function and homology information alkali metal ion binding / lactose catabolic process / beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / carbohydrate binding / magnesium ion binding / identical protein binding Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.66 Å | |||||||||
Authors | McSweeney DM / McSweeney SM / Liu Q | |||||||||
Citation | Journal: IUCrJ / Year: 2020 Title: A self-supervised workflow for particle picking in cryo-EM. Authors: Donal M McSweeney / Sean M McSweeney / Qun Liu / Abstract: High-resolution single-particle cryo-EM data analysis relies on accurate particle picking. To facilitate the particle picking process, a self-supervised workflow has been developed. This includes an ...High-resolution single-particle cryo-EM data analysis relies on accurate particle picking. To facilitate the particle picking process, a self-supervised workflow has been developed. This includes an iterative strategy, which uses a 2D class average to improve training particles, and a progressively improved convolutional neural network for particle picking. To automate the selection of particles, a threshold is defined (%/Res) using the ratio of percentage class distribution and resolution as a cutoff. This workflow has been tested using six publicly available data sets with different particle sizes and shapes, and can automatically pick particles with minimal user input. The picked particles support high-resolution reconstructions at 3.0 Å or better. This workflow is a step towards automated single-particle cryo-EM data analysis at the stage of particle picking. It may be used in conjunction with commonly used single-particle analysis packages such as , , , and . | |||||||||
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_22025.map.gz | 11 MB | EMDB map data format | |
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Header (meta data) | emd-22025-v30.xml emd-22025.xml | 8.5 KB 8.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22025_fsc.xml | 8.7 KB | Display | FSC data file |
Images | emd_22025.png | 301.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22025 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22025 | HTTPS FTP |
-Validation report
Summary document | emd_22025_validation.pdf.gz | 78.6 KB | Display | EMDB validaton report |
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Full document | emd_22025_full_validation.pdf.gz | 77.7 KB | Display | |
Data in XML | emd_22025_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22025 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22025 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_22025.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | beta-galactosidase | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.885 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Escherichia coli beta-galactosidase bound to phenylethyl beta-D-t...
Entire | Name: Escherichia coli beta-galactosidase bound to phenylethyl beta-D-thiogalactopyranoside (PETG) |
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Components |
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-Supramolecule #1: Escherichia coli beta-galactosidase bound to phenylethyl beta-D-t...
Supramolecule | Name: Escherichia coli beta-galactosidase bound to phenylethyl beta-D-thiogalactopyranoside (PETG) type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | JEOL CRYO ARM 200 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 70.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |