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Yorodumi- EMDB-0529: Purified ribosome - A complete data processing workflow for CryoE... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0529 | |||||||||
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Title | Purified ribosome - A complete data processing workflow for CryoET and subtomogram averaging | |||||||||
Map data | Averaged structure of purified ribosome from EMPIAR-10064 dataset, after subtilt refinement in EMAN2. | |||||||||
Sample |
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Biological species | Oryctolagus cuniculus (rabbit) | |||||||||
Method | electron tomography / cryo EM / Resolution: 8.4 Å | |||||||||
Authors | Chen M / Bell JM / Ludtke SJ | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Methods / Year: 2019 Title: A complete data processing workflow for cryo-ET and subtomogram averaging. Authors: Muyuan Chen / James M Bell / Xiaodong Shi / Stella Y Sun / Zhao Wang / Steven J Ludtke / Abstract: Electron cryotomography is currently the only method capable of visualizing cells in three dimensions at nanometer resolutions. While modern instruments produce massive amounts of tomography data ...Electron cryotomography is currently the only method capable of visualizing cells in three dimensions at nanometer resolutions. While modern instruments produce massive amounts of tomography data containing extremely rich structural information, data processing is very labor intensive and the results are often limited by the skills of the personnel rather than the data. We present an integrated workflow that covers the entire tomography data processing pipeline, from automated tilt series alignment to subnanometer resolution subtomogram averaging. Resolution enhancement is made possible through the use of per-particle per-tilt contrast transfer function correction and alignment. The workflow greatly reduces human bias, increases throughput and more closely approaches data-limited resolution for subtomogram averaging in both purified macromolecules and cells. | |||||||||
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_0529.map.gz | 4.4 MB | EMDB map data format | |
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Header (meta data) | emd-0529-v30.xml emd-0529.xml | 10.6 KB 10.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0529_fsc.xml | 6.6 KB | Display | FSC data file |
Images | emd_0529.png | 85.9 KB | ||
Others | emd_0529_additional.map.gz | 21 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0529 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0529 | HTTPS FTP |
-Validation report
Summary document | emd_0529_validation.pdf.gz | 79 KB | Display | EMDB validaton report |
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Full document | emd_0529_full_validation.pdf.gz | 78.1 KB | Display | |
Data in XML | emd_0529_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0529 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0529 | HTTPS FTP |
-Related 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_0529.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Averaged structure of purified ribosome from EMPIAR-10064 dataset, after subtilt refinement in EMAN2. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.62 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Averaged structure after subtomogram refinement but before subtilt...
File | emd_0529_additional.map | ||||||||||||
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Annotation | Averaged structure after subtomogram refinement but before subtilt refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Ribosome from EMPIAR-10064, MixedCTEM dataset
Entire | Name: Ribosome from EMPIAR-10064, MixedCTEM dataset |
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Components |
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-Supramolecule #1: Ribosome from EMPIAR-10064, MixedCTEM dataset
Supramolecule | Name: Ribosome from EMPIAR-10064, MixedCTEM dataset / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
Sectioning | Other: NO SECTIONING |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |