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Yorodumi- EMDB-16056: Electron cryotomogram of septal region from FIB milled filament o... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16056 | ||||||||||||
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Title | Electron cryotomogram of septal region from FIB milled filament of Nostoc sp. PCC 7120 sepN mutant | ||||||||||||
Map data | |||||||||||||
Sample |
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Biological species | Nostoc sp. PCC 7120 = FACHB-418 (bacteria) | ||||||||||||
Method | electron tomography / cryo EM | ||||||||||||
Authors | Kieninger A / Tokarz P / Janovic A / Pilhofer M / Weiss G / Maldener I | ||||||||||||
Funding support | Germany, 3 items
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Citation | Journal: To Be Published Title: Subtomogram average of open state septal junctions from Nostoc PCC 7120 Authors: Kieninger A / Tokarz P / Janovic A / Pilhofer M / Weiss G / Maldener I | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16056.map.gz | 849.4 MB | EMDB map data format | |
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Header (meta data) | emd-16056-v30.xml emd-16056.xml | 8.6 KB 8.6 KB | Display Display | EMDB header |
Images | emd_16056.png | 225.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16056 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16056 | HTTPS FTP |
-Validation report
Summary document | emd_16056_validation.pdf.gz | 453.5 KB | Display | EMDB validaton report |
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Full document | emd_16056_full_validation.pdf.gz | 453.1 KB | Display | |
Data in XML | emd_16056_validation.xml.gz | 5 KB | Display | |
Data in CIF | emd_16056_validation.cif.gz | 5.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16056 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16056 | HTTPS FTP |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_16056.map.gz / Format: CCP4 / Size: 914.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 13.52 Å | ||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : The septal region from FIB milled filament of Nostoc sp. PCC 7120...
Entire | Name: The septal region from FIB milled filament of Nostoc sp. PCC 7120 sepN mutant |
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Components |
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-Supramolecule #1: The septal region from FIB milled filament of Nostoc sp. PCC 7120...
Supramolecule | Name: The septal region from FIB milled filament of Nostoc sp. PCC 7120 sepN mutant type: complex / Chimera: Yes / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 / Details: BG11 broth |
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Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 298.15 K / Instrument: FEI VITROBOT MARK IV |
Details | Thin lamellae through plunge-frozen Nostoc filaments |
Sectioning | Focused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 3 kV / Focused ion beam - Current: 0.058 nA / Focused ion beam - Duration: 1500 sec. / Focused ion beam - Temperature: 123 K / Focused ion beam - Initial thickness: 3000 nm / Focused ion beam - Final thickness: 200 nm Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Zeiss Crossbeam 550. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.1 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 8.0 µm / Nominal defocus min: 8.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Software - Name: Dynamo / Number images used: 61 |
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