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- EMDB-33905: the cryo-EM structure of 50S ribosome -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-33905
Titlethe cryo-EM structure of 50S ribosome
Map data
Sample
  • Complex: 50S ribosome
Keywords50s ribosome / RIBOSOME
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsDamu W / Ning G
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31725007 China
CitationJournal: To Be Published
Title: the cryo-EM structure of 50S ribosome
Authors: Damu W / Ning G
History
DepositionJul 25, 2022-
Header (metadata) releaseAug 9, 2023-
Map releaseAug 9, 2023-
UpdateAug 9, 2023-
Current statusAug 9, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33905.png

Downloads & links

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Map

FileDownload / File: emd_33905.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 300 pix.
= 315.6 Å		1.05 Å/pix.
x 300 pix.
= 315.6 Å		1.05 Å/pix.
x 300 pix.
= 315.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.052 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.07318261 - 2.649688
Average (Standard dev.)0.004852112 (±0.050008606)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 315.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_33905_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_33905_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 50S ribosome

EntireName: 50S ribosome
Components
  • Complex: 50S ribosome

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Supramolecule #1: 50S ribosome

SupramoleculeName: 50S ribosome / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 8.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: DIFFRACTION / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 93913
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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