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- EMDB-19425: Low-dose cryo-electron ptychographic reconstruction of apoferriti... -

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Basic information

Entry
Database: EMDB / ID: EMD-19425
TitleLow-dose cryo-electron ptychographic reconstruction of apoferritin recorded with CSA of 4.0 mrad
Map datasharpened map
Sample
  • Complex: ApoferritinFerritin
KeywordsApoFerritin / METAL BINDING PROTEIN
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.8 Å
AuthorsMohammed I / Stalhberg H / Kucukoglu B
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation200021_200628 Switzerland
CitationJournal: To Be Published
Title: Low-dose cryo-electron ptychography at sub-nanometer resolution of proteins
Authors: Mohammed I / Stalhberg H / Kucukoglu B
History
DepositionJan 17, 2024-
Header (metadata) releaseMay 22, 2024-
Map releaseMay 22, 2024-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19425.png

Downloads & links

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Map

FileDownload / File: emd_19425.map.gz / Format: CCP4 / Size: 13.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Voxel sizeX=Y=Z: 1.5 Å
Density
Contour LevelBy AUTHOR: 0.544
Minimum - Maximum-2.0024998 - 3.2870882
Average (Standard dev.)-0.0036878418 (±0.24388203)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions154154154
Spacing154154154
CellA=B=C: 231.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19425_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_19425_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_19425_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 : Apoferritin

EntireName: ApoferritinFerritin
Components
  • Complex: ApoferritinFerritin

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Supramolecule #1: Apoferritin

SupramoleculeName: Apoferritin / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 480 KDa

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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

Concentration5 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 1.7 µm / Nominal defocus min: 1.4000000000000001 µm
Image recordingFilm or detector model: DECTRIS ELA (1k x 0.5k) / Average electron dose: 32.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE / Details: ab-initio
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1) / Details: point group symmetry applied:O
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1) / Details: point group symmetry applied:O
Final reconstructionApplied symmetry - Point group: O (octahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1) / Number images used: 11552
Detailspy4DSTEM cryoSPARC
FSC plot (resolution estimation)

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