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- EMDB-71629: Comparison of fully-sampled and sparse cryo-STEM tomography 3D re... -

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Basic information

Entry
Database: EMDB / ID: EMD-71629
TitleComparison of fully-sampled and sparse cryo-STEM tomography 3D reconstructions
Map data3D SIRT reconstruction of DCT inpainted sparse (66%) cryo-STEM tilt-series on E. coli cell 1
Sample
  • Cell: Whole E. coli cryo-tomography
KeywordsE. coli / bacteria / UNKNOWN FUNCTION
Biological speciesEscherichia coli (E. coli)
Methodelectron tomography / cryo EM
AuthorsTrepout S
Funding support France, 1 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-21-CE42-0001 France
CitationJournal: To Be Published
Title: Comparison of fully-sampled and sparse cryo-STEM tomography 3D reconstructions
Authors: Trepout S
History
DepositionJul 7, 2025-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71629.png

Downloads & links

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Map

FileDownload / File: emd_71629.map.gz / Format: CCP4 / Size: 683.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D SIRT reconstruction of DCT inpainted sparse (66%) cryo-STEM tilt-series on E. coli cell 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
40 Å/pix.
x 400 pix.
= 16000. Å		40 Å/pix.
x 700 pix.
= 28000. Å		40 Å/pix.
x 640 pix.
= 25600. 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: 40 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-4.617276 - 1.3960353
Average (Standard dev.)0.13880327 (±0.2459189)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-50
Dimensions700640400
Spacing640700400
CellA: 25600.0 Å / B: 28000.0 Å / C: 16000.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: 3D SIRT reconstruction of fully-sampled cryo-STEM tilt-series on...

Fileemd_71629_additional_1.map
Annotation3D SIRT reconstruction of fully-sampled cryo-STEM tilt-series on E. coli cell 4
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 3D SIRT reconstruction of DCT inpainted sparse (75%)...

Fileemd_71629_additional_10.map
Annotation3D SIRT reconstruction of DCT inpainted sparse (75%) cryo-STEM tilt-series on E. coli cell 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 3D SIRT reconstruction of fully-sampled cryo-STEM tilt-series on...

Fileemd_71629_additional_11.map
Annotation3D SIRT reconstruction of fully-sampled cryo-STEM tilt-series on E. coli cell 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 3D SIRT reconstruction of fully-sampled cryo-STEM tilt-series on...

Fileemd_71629_additional_2.map
Annotation3D SIRT reconstruction of fully-sampled cryo-STEM tilt-series on E. coli cell 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 3D SIRT reconstruction of DCT inpainted sparse (66%)...

Fileemd_71629_additional_3.map
Annotation3D SIRT reconstruction of DCT inpainted sparse (66%) cryo-STEM tilt-series on E. coli cell 4
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 3D SIRT reconstruction of DCT inpainted sparse (75%)...

Fileemd_71629_additional_4.map
Annotation3D SIRT reconstruction of DCT inpainted sparse (75%) cryo-STEM tilt-series on E. coli cell 5
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 3D SIRT reconstruction of fully-sampled cryo-STEM tilt-series on...

Fileemd_71629_additional_5.map
Annotation3D SIRT reconstruction of fully-sampled cryo-STEM tilt-series on E. coli cell 5
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 3D SIRT reconstruction of DCT inpainted sparse (80%)...

Fileemd_71629_additional_6.map
Annotation3D SIRT reconstruction of DCT inpainted sparse (80%) cryo-STEM tilt-series on E. coli cell 6
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 3D SIRT reconstruction of fully-sampled cryo-STEM tilt-series on...

Fileemd_71629_additional_7.map
Annotation3D SIRT reconstruction of fully-sampled cryo-STEM tilt-series on E. coli cell 6
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 3D SIRT reconstruction of DCT inpainted sparse (80%)...

Fileemd_71629_additional_8.map
Annotation3D SIRT reconstruction of DCT inpainted sparse (80%) cryo-STEM tilt-series on E. coli cell 3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 3D SIRT reconstruction of fully-sampled cryo-STEM tilt-series on...

Fileemd_71629_additional_9.map
Annotation3D SIRT reconstruction of fully-sampled cryo-STEM tilt-series on E. coli cell 3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Whole E. coli cryo-tomography

EntireName: Whole E. coli cryo-tomography
Components
  • Cell: Whole E. coli cryo-tomography

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Supramolecule #1: Whole E. coli cryo-tomography

SupramoleculeName: Whole E. coli cryo-tomography / type: cell / 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
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.4 / Details: M9 media
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Instrument: LEICA EM CPC
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Aurion / Diameter: 20 nm

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Electron microscopy

MicroscopeJEOL 2200FS
DetailsAlignment on the Ronchigram
Image recordingFilm or detector model: OTHER / Detector mode: COUNTING / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.5 µm / Nominal defocus min: 0.2 µm
Sample stageSpecimen holder model: GATAN 914 HIGH TILT LIQUID NITROGEN CRYO TRANSFER TOMOGRAPHY HOLDER
Cooling holder cryogen: NITROGEN

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Image processing

DetailsJEOL BF STEM Detector
Final reconstructionAlgorithm: SIMULTANEOUS ITERATIVE (SIRT) / Software - Name: TOMO3D / Number images used: 40
CTF correctionDetails: This is STEM / Type: NONE

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