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Yorodumi- EMDB-29780: Cryo-Electron Tomography of a Cryo-Lamella cut inside a Mouse Kid... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29780 | ||||||||||||
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Title | Cryo-Electron Tomography of a Cryo-Lamella cut inside a Mouse Kidney Tissue Biopsy | ||||||||||||
Map data | Cryo-Electron Tomography of Mouse Kidney Tissue Biopsy | ||||||||||||
Sample |
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Keywords | Microtubules / mitochondria / UNKNOWN FUNCTION | ||||||||||||
Biological species | Mus musculus (house mouse) | ||||||||||||
Method | electron tomography | ||||||||||||
Authors | Trepout S / Ramm G | ||||||||||||
Funding support | Australia, United States, 3 items
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Citation | Journal: To Be Published Title: Cryo-Electron Tomography of a Cryo-Lamella Milled Inside a Mouse Kidney Tissue Biopsy Authors: Trepout S / Ramm G | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29780.map.gz | 4.3 GB | EMDB map data format | |
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Header (meta data) | emd-29780-v30.xml emd-29780.xml | 8.9 KB 8.9 KB | Display Display | EMDB header |
Images | emd_29780.png | 236.5 KB | ||
Filedesc metadata | emd-29780.cif.gz | 3.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29780 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29780 | HTTPS FTP |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_29780.map.gz / Format: CCP4 / Size: 4.6 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||
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Annotation | Cryo-Electron Tomography of Mouse Kidney Tissue Biopsy | ||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 14.66 Å | ||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Biopsy of Mouse Kidney Tissue
Entire | Name: Biopsy of Mouse Kidney Tissue |
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Components |
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-Supramolecule #1: Biopsy of Mouse Kidney Tissue
Supramolecule | Name: Biopsy of Mouse Kidney Tissue / type: tissue / ID: 1 / Parent: 0 Details: Cryo-lamella cut inside the biopsy using the bbq method. |
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Source (natural) | Organism: Mus musculus (house mouse) / Organ: kidney |
-Experimental details
-Structure determination
Processing | electron tomography |
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Aggregation state | tissue |
-Sample preparation
Buffer | pH: 6.9 |
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High pressure freezing | Instrument: OTHER Details: The value given for _em_high_pressure_freezing.instrument is HPF Wohlwend Compact 03. This is not in a list of allowed values {'LEICA EM HPM100', 'LEICA EM PACT2', 'OTHER', 'EMS-002 RAPID ...Details: The value given for _em_high_pressure_freezing.instrument is HPF Wohlwend Compact 03. This is not in a list of allowed values {'LEICA EM HPM100', 'LEICA EM PACT2', 'OTHER', 'EMS-002 RAPID IMMERSION FREEZER', 'LEICA EM PACT', 'BAL-TEC HPM 010'} so OTHER is written into the XML file. |
Sectioning | Focused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 1 / Focused ion beam - Duration: 1800 / Focused ion beam - Temperature: 100 K / Focused ion beam - Initial thickness: 100000 / Focused ion beam - Final thickness: 250 Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is FEI Helios G4 UX. This is not in a list of allowed values {'OTHER', 'DB235'} so OTHER is written into the XML file. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4.0 µm / Nominal defocus min: 4.0 µm |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.5 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: BACK PROJECTION / Software - Name: IMOD / Details: Tilt-series alignment performed in AreTomo v1.0.1 / Number images used: 59 |
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