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- EMDB-57021: Optimal tilt-increment for cryo-ET -

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Basic information

Entry
Database: EMDB / ID: EMD-57021
TitleOptimal tilt-increment for cryo-ET
Map dataRibosome from Dictyostelium discoideum, from in-situ data using cryo-ET and STA. Acquired with a 3-degree tilt-increment. Refined with M.
Sample
  • Cell: Dictyostelium discoideum
KeywordsRibosome / cryo-electron tomography / subtomogram averaging
Biological speciesDictyostelium discoideum AX2 (eukaryote)
Methodsubtomogram averaging / cryo EM / Resolution: 5.8 Å
AuthorsTuijtel MW / Beck M
Funding support United States, 1 items
OrganizationGrant numberCountry
Chan Zuckerberg Initiative2021-234666 United States
Citation
Journal: Elife / Year: 2026
Title: Optimising the tilt increment for in situ cryo-electron tomography.
Authors: Maarten Willem Tuijtel / Tomáš Majtner / Beata Turoňová / Martin Beck /
Abstract: Cryo-electron tomography (cryo-ET) enables high-resolution, three-dimensional imaging of cellular structures in their native, frozen state. However, image quality is limited by a trade-off between ...Cryo-electron tomography (cryo-ET) enables high-resolution, three-dimensional imaging of cellular structures in their native, frozen state. However, image quality is limited by a trade-off between angular sampling and radiation damage. Therefore, the choice of the angular increment during data collection is a critical parameter that affects tomogram quality and downstream analyses. Optimising this increment is challenging due to the high demands on microscope time, storage, and computation. In this study, we systematically evaluated tilt increments of 1°, 2°, 3°, 5°, and 10° using lamellae from cells. We found that at a constant total electron dose, finer tilt increments (1-3°) produced better-aligned tomograms with higher signal-to-noise ratios and improved outcomes in template matching and subtomogram averaging. A 3° increment emerged as the optimal balance between data quality, alignment accuracy, dose per image, and processing efficiency. This practical recommendation supports both high-throughput and high-resolution structural studies and can guide future cryo-ET data acquisition strategies.
#1: Journal: Elife / Year: 2026
Title: Optimising the tilt-increment for in situ cryo-electron tomography
Authors: Tuijtel MW / Majtner T / Turonova B / Beck M
History
DepositionMar 3, 2026-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_57021.png

Downloads & links

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Map

FileDownload / File: emd_57021.map.gz / Format: CCP4 / Size: 172.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRibosome from Dictyostelium discoideum, from in-situ data using cryo-ET and STA. Acquired with a 3-degree tilt-increment. Refined with M.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.97 Å/pix.
x 356 pix.
= 701.676 Å		1.97 Å/pix.
x 356 pix.
= 701.676 Å		1.97 Å/pix.
x 356 pix.
= 701.676 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.971 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00275
Minimum - Maximum-0.0035371208 - 0.009554365
Average (Standard dev.)0.000028690183 (±0.00047960176)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions356356356
Spacing356356356
CellA=B=C: 701.67596 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Ribosome from Dictyostelium discoideum. Acquired with a 3-degree...

Fileemd_57021_additional_1.map
AnnotationRibosome from Dictyostelium discoideum. Acquired with a 3-degree tilt-increment. Refined with M, local resolution.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Ribosome from Dictyostelium discoideum. Acquired with a 1-degree...

Fileemd_57021_additional_2.map
AnnotationRibosome from Dictyostelium discoideum. Acquired with a 1-degree tilt-increment. Refined with M.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Ribosome from Dictyostelium discoideum. Acquired with a 2-degree...

Fileemd_57021_additional_3.map
AnnotationRibosome from Dictyostelium discoideum. Acquired with a 2-degree tilt-increment. Refined with M, local resolution.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Ribosome from Dictyostelium discoideum. Acquired with a 10-degree...

Fileemd_57021_additional_4.map
AnnotationRibosome from Dictyostelium discoideum. Acquired with a 10-degree tilt-increment. Refined with M, local resolution.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Ribosome from Dictyostelium discoideum. Acquired with a 2-degree...

Fileemd_57021_additional_5.map
AnnotationRibosome from Dictyostelium discoideum. Acquired with a 2-degree tilt-increment. Refined with M.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Ribosome from Dictyostelium discoideum. Acquired with a 10-degree...

Fileemd_57021_additional_6.map
AnnotationRibosome from Dictyostelium discoideum. Acquired with a 10-degree tilt-increment. Refined with M.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Ribosome from Dictyostelium discoideum. Acquired with a 1-degree...

Fileemd_57021_additional_7.map
AnnotationRibosome from Dictyostelium discoideum. Acquired with a 1-degree tilt-increment. Refined with M, local resolution.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Ribosome from Dictyostelium discoideum. Acquired with a 5-degree...

Fileemd_57021_additional_8.map
AnnotationRibosome from Dictyostelium discoideum. Acquired with a 5-degree tilt-increment. Refined with M, local resolution.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Ribosome from Dictyostelium discoideum. Acquired with a 5-degree...

Fileemd_57021_additional_9.map
AnnotationRibosome from Dictyostelium discoideum. Acquired with a 5-degree tilt-increment. Refined with M.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Half map: Ribosome from Dictyostelium discoideum. Acquired with a 3-degree...

Fileemd_57021_half_map_1.map
AnnotationRibosome from Dictyostelium discoideum. Acquired with a 3-degree tilt-increment. Refined with M. Halfmap 2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Half map: Ribosome from Dictyostelium discoideum. Acquired with a 3-degree...

Fileemd_57021_half_map_2.map
AnnotationRibosome from Dictyostelium discoideum. Acquired with a 3-degree tilt-increment. Refined with M. Halfmap 1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dictyostelium discoideum

EntireName: Dictyostelium discoideum (eukaryote)
Components
  • Cell: Dictyostelium discoideum

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Supramolecule #1: Dictyostelium discoideum

SupramoleculeName: Dictyostelium discoideum / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Dictyostelium discoideum AX2 (eukaryote)

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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 / Details: HL5 medium
GridModel: Quantifoil / Material: GOLD / Mesh: 200 / Support film - Material: SILICON DIOXIDE / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 38.0 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 21 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 6 / Average electron dose: 3.2 e/Å2
Details: Value for electron dose varied with the tilt-increment
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 81000
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

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: M / Number subtomograms used: 10760
ExtractionNumber tomograms: 20 / Number images used: 22303 / Software - Name: Warp
CTF correctionType: PHASE FLIPPING ONLY
Final angle assignmentType: MAXIMUM LIKELIHOOD

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