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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Tomogram 4 - Thickness measurement | |||||||||
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![]() | ER-HOXB8 cells / neutrophils / cytoplasm / RIBOSOME | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | electron tomography / cryo EM | |||||||||
![]() | Elferich J / Kong L / Zottig X / Grigorieff N | |||||||||
Funding support | ![]()
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![]() | ![]() Title: CTFFIND5 provides improved insight into quality, tilt and thickness of TEM sample Authors: Elferich J / Kong L / Zottig X / Grigorieff N | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 865.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 7.5 KB 7.5 KB | Display Display | ![]() |
Images | ![]() | 131.4 KB | ||
Filedesc metadata | ![]() | 3.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 448.9 KB | Display | ![]() |
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Full document | ![]() | 448.4 KB | Display | |
Data in XML | ![]() | 10.5 KB | Display | |
Data in CIF | ![]() | 13.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Voxel size | X=Y=Z: 8.349 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
-Entire : ER-HOXB8 sample prepared by FIB_SEM milling
Entire | Name: ER-HOXB8 sample prepared by FIB_SEM milling |
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Components |
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-Supramolecule #1: ER-HOXB8 sample prepared by FIB_SEM milling
Supramolecule | Name: ER-HOXB8 sample prepared by FIB_SEM milling / type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | electron tomography |
Aggregation state | cell |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Instrument: LEICA PLUNGER |
Sectioning | Focused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.03 / Focused ion beam - Duration: 60 / Focused ion beam - Temperature: 273 K / Focused ion beam - Initial thickness: 1000 / Focused ion beam - Final thickness: 200 Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Aquilos 2. This is not in a list of allowed values {'OTHER', 'DB235'} so OTHER is written into the XML file. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 8.0 µm / Nominal defocus min: 6.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Algorithm: SIMULTANEOUS ITERATIVE (SIRT) / Resolution method: OTHER / Number images used: 35 |
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