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- EMDB-4698: Mouse apoferritin from data collected at liquid helium temperature -

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Basic information

Database: EMDB / ID: EMD-4698
TitleMouse apoferritin from data collected at liquid helium temperatureFerritin
Map data
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsPfeil-Gardiner O / Mills DJ / Vonck J / Kuehlbrandt W
CitationJournal: IUCrJ / Year: 2019
Title: A comparative study of single-particle cryo-EM with liquid-nitrogen and liquid-helium cooling.
Authors: Olivia Pfeil-Gardiner / Deryck J Mills / Janet Vonck / Werner Kuehlbrandt /
Abstract: Radiation damage is the most fundamental limitation for achieving high resolution in electron cryo-microscopy (cryo-EM) of biological samples. The effects of radiation damage are reduced by liquid- ...Radiation damage is the most fundamental limitation for achieving high resolution in electron cryo-microscopy (cryo-EM) of biological samples. The effects of radiation damage are reduced by liquid-helium cooling, although the use of liquid helium is more challenging than that of liquid nitrogen. To date, the benefits of liquid-nitrogen and liquid-helium cooling for single-particle cryo-EM have not been compared quantitatively. With recent technical and computational advances in cryo-EM image recording and processing, such a comparison now seems timely. This study aims to evaluate the relative merits of liquid-helium cooling in present-day single-particle analysis, taking advantage of direct electron detectors. Two data sets for recombinant mouse heavy-chain apoferritin cooled with liquid-nitrogen or liquid-helium to 85 or 17 K were collected, processed and compared. No improvement in terms of resolution or Coulomb potential map quality was found for liquid-helium cooling. Interestingly, beam-induced motion was found to be significantly higher with liquid-helium cooling, especially within the most valuable first few frames of an exposure, thus counteracting any potential benefit of better cryoprotection that liquid-helium cooling may offer for single-particle cryo-EM.
DepositionMar 13, 2019-
Header (metadata) releaseMar 27, 2019-
Map releaseMar 27, 2019-
UpdateNov 20, 2019-
Current statusNov 20, 2019Processing site: PDBe / Status: Released

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.038
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.038
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
Supplemental images

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FileDownload / File: emd_4698.map.gz / Format: CCP4 / Size: 20.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 176 pix.
= 197.12 Å
1.12 Å/pix.
x 176 pix.
= 197.12 Å
1.12 Å/pix.
x 176 pix.
= 197.12 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.12 Å
Contour LevelBy AUTHOR: 0.038 / Movie #1: 0.038
Minimum - Maximum-0.14564039 - 0.22997136
Average (Standard dev.)0.00000001640 (±0.016055685)
SymmetrySpace group: 1


Map geometry
Axis orderXYZ
CellA=B=C: 197.12 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.121.121.12
M x/y/z176176176
origin x/y/z0.0000.0000.000
length x/y/z197.120197.120197.120
start NX/NY/NZ929262
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.1460.2300.000

Supplemental data

Sample components

Entire apoferritin

EntireName: apoferritinFerritin / Number of components: 1

Component #1: protein, apoferritin

ProteinName: apoferritinFerritin / Recombinant expression: No
MassTheoretical: 500 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Escherichia coli (E. coli)

Experimental details

Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 1.5 mg/mL / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 283 K / Humidity: 100 %

Electron microscopy imaging

ImagingMicroscope: JEOL 3200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 72 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 30000.0 X (nominal), 44642.0 X (calibrated) / Cs: 4.2 mm / Imaging mode: BRIGHT FIELD / Energy filter: In-column Omega Filter
Specimen HolderModel: JEOL / Temperature: (17.0 - 17.0 K)
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 233

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: O (octahedral) / Number of projections: 190785
3D reconstructionSoftware: RELION / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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