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- EMDB-18197: Subtomogram average of Ribosome from S.cerevisiae prepared using ... -

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Basic information

Entry
Database: EMDB / ID: EMD-18197
TitleSubtomogram average of Ribosome from S.cerevisiae prepared using cryo-plasmaFIB milling
Map dataPostprocessed density map TOMOMAN-STOPGAP-Warp-Relion3-M
Sample
  • Complex: 80S S. cerevisiae
Keywordsyeast 80S / RIBOSOME
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsubtomogram averaging / cryo EM / Resolution: 4.3 Å
AuthorsKhavnekar S / Kelley R / Plitzko J / Kotecha A
Funding support Germany, 2 items
OrganizationGrant numberCountry
Max Planck Society Germany
Other private
CitationJournal: To Be Published
Title: In situ cryo-ET of S. cerevisiae prepared using cryo-plasmaFIB milling
Authors: Khavnekar S / Kelley R / Plitzko J / Kotecha A
History
DepositionAug 14, 2023-
Header (metadata) releaseAug 23, 2023-
Map releaseAug 23, 2023-
UpdateAug 23, 2023-
Current statusAug 23, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18197.png

Downloads & links

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Map

FileDownload / File: emd_18197.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed density map TOMOMAN-STOPGAP-Warp-Relion3-M
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.96 Å/pix.
x 256 pix.
= 501.76 Å		1.96 Å/pix.
x 256 pix.
= 501.76 Å		1.96 Å/pix.
x 256 pix.
= 501.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.575
Minimum - Maximum-0.67401004 - 2.303343
Average (Standard dev.)-0.002233052 (±0.15266797)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 501.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18197_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map TOMOMAN-STOPGAP-Warp-Relion3-M

Fileemd_18197_half_map_1.map
Annotationhalf-map TOMOMAN-STOPGAP-Warp-Relion3-M
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map TOMOMAN-STOPGAP-Warp-Relion3-M

Fileemd_18197_half_map_2.map
Annotationhalf-map TOMOMAN-STOPGAP-Warp-Relion3-M
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 80S S. cerevisiae

EntireName: 80S S. cerevisiae
Components
  • Complex: 80S S. cerevisiae

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Supramolecule #1: 80S S. cerevisiae

SupramoleculeName: 80S S. cerevisiae / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 3.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 119031
ExtractionNumber tomograms: 250 / Number images used: 250000
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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