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- EMDB-16056: Electron cryotomogram of septal region from FIB milled filament o... -

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Basic information

Entry
Database: EMDB / ID: EMD-16056
TitleElectron cryotomogram of septal region from FIB milled filament of Nostoc sp. PCC 7120 sepN mutant
Map data
Sample
  • Complex: The septal region from FIB milled filament of Nostoc sp. PCC 7120 sepN mutant
Biological speciesNostoc sp. PCC 7120 = FACHB-418 (bacteria)
Methodelectron tomography / cryo EM
AuthorsKieninger A / Tokarz P / Janovic A / Pilhofer M / Weiss G / Maldener I
Funding support Germany, 3 items
OrganizationGrant numberCountry
German Research Foundation (DFG)GRK1708 Germany
Boehringer Ingelheim Fonds (BIF) Germany
Other government
CitationJournal: 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
DepositionOct 31, 2022-
Header (metadata) releaseNov 23, 2022-
Map releaseNov 23, 2022-
UpdateDec 7, 2022-
Current statusDec 7, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16056.png

Downloads & links

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Map

FileDownload / File: emd_16056.map.gz / Format: CCP4 / Size: 914.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
13.52 Å/pix.
x 269 pix.
= 3636.88 Å		13.52 Å/pix.
x 928 pix.
= 12546.561 Å		13.52 Å/pix.
x 960 pix.
= 12979.2 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 13.52 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-183.93195 - 154.37904
Average (Standard dev.)-5.8958216e-10 (±13.0436)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions928960269
Spacing960928269
CellA: 12979.2 Å / B: 12546.561 Å / C: 3636.8801 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : The septal region from FIB milled filament of Nostoc sp. PCC 7120...

EntireName: The septal region from FIB milled filament of Nostoc sp. PCC 7120 sepN mutant
Components
  • Complex: The septal region from FIB milled filament of Nostoc sp. PCC 7120 sepN mutant

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Supramolecule #1: The septal region from FIB milled filament of Nostoc sp. PCC 7120...

SupramoleculeName: The septal region from FIB milled filament of Nostoc sp. PCC 7120 sepN mutant
type: complex / Chimera: Yes / ID: 1 / Parent: 0
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.4 / Details: BG11 broth
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 298.15 K / Instrument: FEI VITROBOT MARK IV
DetailsThin lamellae through plunge-frozen Nostoc filaments
SectioningFocused 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.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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

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Image processing

Final reconstructionSoftware - Name: Dynamo / Number images used: 61

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