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- EMDB-43428: Tomogram 6 - Thickness measurement -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-43428
TitleTomogram 6 - Thickness measurement
Map data
Sample
  • Cell: ER-HOXB8 sample prepared by FIB_SEM milling
KeywordsER-HOXB8 cells / neutrophils / cytoplasm / RIBOSOME
Biological speciesMus musculus (house mouse)
Methodelectron tomography / cryo EM
AuthorsElferich J / Kong L / Zottig X / Grigorieff N
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Elife / Year: 2024
Title: CTFFIND5 provides improved insight into quality, tilt and thickness of TEM sample
Authors: Elferich J / Kong L / Zottig X / Grigorieff N
History
DepositionJan 17, 2024-
Header (metadata) releaseJan 31, 2024-
Map releaseJan 31, 2024-
UpdateAug 21, 2024-
Current statusAug 21, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43428.png

Downloads & links

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Map

FileDownload / File: emd_43428.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.35 Å/pix.
x 1440 pix.
= 12022.56 Å		8.35 Å/pix.
x 625 pix.
= 5218.125 Å		8.35 Å/pix.
x 1024 pix.
= 8549.376 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: 8.349 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-85.0 - 92.0
Average (Standard dev.)6.0640793 (±11.324092)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-312208-209
Dimensions62510241440
Spacing10246251440
CellA: 8549.376 Å / B: 5218.125 Å / C: 12022.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : ER-HOXB8 sample prepared by FIB_SEM milling

EntireName: ER-HOXB8 sample prepared by FIB_SEM milling
Components
  • Cell: ER-HOXB8 sample prepared by FIB_SEM milling

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Supramolecule #1: ER-HOXB8 sample prepared by FIB_SEM milling

SupramoleculeName: ER-HOXB8 sample prepared by FIB_SEM milling / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)

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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: 7.5
VitrificationCryogen name: ETHANE / Instrument: LEICA PLUNGER
SectioningFocused 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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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 reconstructionAlgorithm: SIMULTANEOUS ITERATIVE (SIRT) / Resolution method: OTHER / Number images used: 33

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