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- EMDB-55665: E.coli ribosome reconstruction from frames 1-20, dose weighted -

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Basic information

Entry
Database: EMDB / ID: EMD-55665
TitleE.coli ribosome reconstruction from frames 1-20, dose weighted
Map dataMain map
Sample
  • Complex: E.coli ribosome
Keywordsribosome / electron damage / dose dependency
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.28 Å
AuthorsWazny G / Glatt S / Indyka P / Jaciuk M / Rawski M / Biela AP
Funding support Poland, 1 items
OrganizationGrant numberCountry
Ministry of Science and Higher Education (Poland)1/SOL/2021/2 Poland
CitationJournal: Ultramicroscopy / Year: 2026
Title: Influence of total electron dose on the quality of nucleic acids potential maps in Cryo-EM.
Authors: Grzegorz Ważny / Marcin Jaciuk / Paulina Indyka / Sebastian Glatt / Artur Biela / Michał Rawski /
Abstract: The standardization of protocols in science lies at the basis of every experiment. During this process, some crucial questions need to be answered. The quality of results in single particle cryo- ...The standardization of protocols in science lies at the basis of every experiment. During this process, some crucial questions need to be answered. The quality of results in single particle cryo-Electron Microscopy (cryo-EM) requires optimized data collection parameters. Hence, before each experiment, the following questions need to be defined: (i) which optimal electron dose should be used? (ii) at which level does the accumulated electron damage start to affect resolution? (iii) how does pre-exposure influence the level of damage? (iv) how does dose weighting over the scale of total electron dose deposited to the sample influence the resulting reconstruction? In this manuscript, we addressed all of the above questions by performing a systematic analysis of the relation between data collection strategies and the resulting outcome in the form of cryo-EM map quality of Escherichia coli and H. sapiens ribosome particles. Our findings will serve as references for users seeking to optimize data collection and reconstruction routines for single particle cryo-EM experiments.
History
DepositionNov 12, 2025-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55665.png

Downloads & links

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Map

FileDownload / File: emd_55665.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 512 pix.
= 430.08 Å		0.84 Å/pix.
x 512 pix.
= 430.08 Å		0.84 Å/pix.
x 512 pix.
= 430.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.585
Minimum - Maximum-0.32756194 - 0.7701555
Average (Standard dev.)-0.0003682676 (±0.019499596)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 430.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_55665_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halj map B

Fileemd_55665_half_map_2.map
Annotationhalj map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : E.coli ribosome

EntireName: E.coli ribosome
Components
  • Complex: E.coli ribosome

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Supramolecule #1: E.coli ribosome

SupramoleculeName: E.coli 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: 7.2
GridModel: Quantifoil Active R2/1 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 20.0 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: 2.1 µm / Nominal defocus min: 0.9 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.28 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 149565
Initial angle assignmentType: COMMON LINE / Software - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 1 / Avg.num./class: 150000 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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