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- EMDB-16537: Optimizing Cryo-FIB Lamellas for sub-5 Angstrom in situ Structura... -
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Open data
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Basic information
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Title | Optimizing Cryo-FIB Lamellas for sub-5 Angstrom in situ Structural Biology : Subtomogram average of the Large Subunit of S.Cerevisiae 80S Ribosome | |||||||||
![]() | Local resolution filtered map after M refinement Workflow: TOMOMAN-STOPGAP-Warp-Relion-M | |||||||||
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![]() | S.Cerevisiae / 80S / Ribosome / FIB / insitu | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 4.6 Å | |||||||||
![]() | Khavnekar S / Vrbovska V / Zaoralova M / KElley R / Beck F / Klumpe S / Kotech A / Plitzko JM / Erdmann PS | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Optimizing Cryo-FIB Lamellas for sub-5 Angstrom in situ Structural Biology : Large Subunit of S.Cerevisiae 80S Ribosome Authors: Khavnekar S / Vrbovska V / Zaoralova M / KElley R / Beck F / Klumpe S / Kotech A / Plitzko JM / Erdmann PS | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 222.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 12.1 KB 12.1 KB | Display Display | ![]() |
Images | ![]() | 65.3 KB | ||
Masks | ![]() | 411.4 MB | ![]() | |
Filedesc metadata | ![]() | 4 KB | ||
Others | ![]() ![]() | 212.1 MB 212.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 980 KB | Display | ![]() |
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Full document | ![]() | 979.6 KB | Display | |
Data in XML | ![]() | 17.6 KB | Display | |
Data in CIF | ![]() | 21 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | Local resolution filtered map after M refinement Workflow: TOMOMAN-STOPGAP-Warp-Relion-M | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.6 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: From WARP/M
File | emd_16537_half_map_1.map | ||||||||||||
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Annotation | From WARP/M | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: From WARP/M
File | emd_16537_half_map_2.map | ||||||||||||
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Annotation | From WARP/M | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : S.Cerevisiae 80s ribosome large subunit
Entire | Name: S.Cerevisiae 80s ribosome large subunit |
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Components |
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-Supramolecule #1: S.Cerevisiae 80s ribosome large subunit
Supramolecule | Name: S.Cerevisiae 80s ribosome large subunit / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 3.5 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | subtomogram averaging |
Aggregation state | cell |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
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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: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 12500 |
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Extraction | Number tomograms: 91 / Number images used: 45500 |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |