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- EMDB-25840: 2.19A reconstruction of mouse heavy chain apoferritin collected a... -

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Basic information

Entry
Database: EMDB / ID: EMD-25840
Title2.19A reconstruction of mouse heavy chain apoferritin collected at 720 micrographs/hr
Map datasharp main map
Sample
  • Complex: mouse heavy chain apoferritin
KeywordsMETAL TRANSPORT
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.19 Å
AuthorsPeck JV / Fay JF / Strauss JD
Funding support1 items
OrganizationGrant numberCountry
Other private
CitationJournal: IUCrJ / Year: 2022
Title: High-speed high-resolution data collection on a 200 keV cryo-TEM.
Authors: Jared V Peck / Jonathan F Fay / Joshua D Strauss /
Abstract: Limitations to successful single-particle cryo-electron microscopy (cryo-EM) projects include stable sample generation, production of quality cryo-EM grids with randomly oriented particles embedded ...Limitations to successful single-particle cryo-electron microscopy (cryo-EM) projects include stable sample generation, production of quality cryo-EM grids with randomly oriented particles embedded in thin vitreous ice and access to microscope time. To address the limitation of microscope time, methodologies to more efficiently collect data on a 200 keV Talos Arctica cryo-transmission electron microscope at speeds as fast as 720 movies per hour (∼17 000 per day) were tested. In this study, key parameters were explored to increase data collection speed including: (1) using the beam-image shift method to acquire multiple images per stage position, (2) employing UltrAufoil TEM grids with R0.6/1 hole spacing, (3) collecting hardware-binned data and (4) adjusting the image shift delay factor in . Here, eight EM maps of mouse apoferritin at 1.8-1.9 Å resolution were obtained in the analysis with data collection times for each dataset ranging from 56 min to 2 h. An EM map of mouse apoferritin at 1.78 Å was obtained from an overnight data collection at a speed of 500 movies per hour and subgroup analysis performed, with no significant variation observed in data quality by image shift distance and image shift delay. The findings and operating procedures detailed herein allow for rapid turnover of single-particle cryo-EM structure determination.
History
DepositionJan 3, 2022-
Header (metadata) releaseJan 26, 2022-
Map releaseJan 26, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.63
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.63
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_25840.png

Downloads & links

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Map

FileDownload / File: emd_25840.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharp main map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 256 pix.
= 225.28 Å		0.88 Å/pix.
x 256 pix.
= 225.28 Å		0.88 Å/pix.
x 256 pix.
= 225.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.63 / Movie #1: 0.63
Minimum - Maximum-1.3949387 - 2.159511
Average (Standard dev.)-0.0016738648 (±0.13278462)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 225.28 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.880.880.88
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z225.280225.280225.280
α/β/γ90.00090.00090.000
start NX/NY/NZ535455
NX/NY/NZ134138134
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-1.3952.160-0.002

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Supplemental data

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Half map: Unfiltered half map B

Fileemd_25840_half_map_1.map
AnnotationUnfiltered half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half map B

Fileemd_25840_half_map_2.map
AnnotationUnfiltered half 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 : mouse heavy chain apoferritin

EntireName: mouse heavy chain apoferritin
Components
  • Complex: mouse heavy chain apoferritin

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Supramolecule #1: mouse heavy chain apoferritin

SupramoleculeName: mouse heavy chain apoferritin / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 487.32 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

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 95 %

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 54.3 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.86 µm / Nominal defocus min: 0.46 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE / Details: Ab Initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.19 Å / Resolution method: FSC 0.143 CUT-OFF / Details: Fully independent maps (gold standard) / Number images used: 219350
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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