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- EMDB-4701: Mouse apoferritin from data collected at liquid nitrogen temperature -

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Basic information

Entry
Database: EMDB / ID: EMD-4701
TitleMouse apoferritin from data collected at liquid nitrogen temperature
Map datamouse apoferritin from data collected at liquid nitrogen temperature
Sample
  • Complex: apoferritin
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 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.
History
DepositionMar 13, 2019-
Header (metadata) releaseMar 27, 2019-
Map releaseMar 27, 2019-
UpdateNov 20, 2019-
Current statusNov 20, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.048
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.048
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4701.png

Downloads & links

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Map

FileDownload / File: emd_4701.map.gz / Format: CCP4 / Size: 20.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmouse apoferritin from data collected at liquid nitrogen temperature
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.12 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.048 / Movie #1: 0.048
Minimum - Maximum-0.20449728 - 0.31042898
Average (Standard dev.)-0.0000455770 (±0.020394603)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions176176176
Spacing176176176
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
α/β/γ90.00090.00090.000
start NX/NY/NZ929262
NX/NY/NZ290290360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS176176176
D min/max/mean-0.2040.310-0.000

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Supplemental data

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Sample components

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Entire : apoferritin

EntireName: apoferritin
Components
  • Complex: apoferritin

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Supramolecule #1: apoferritin

SupramoleculeName: apoferritin / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 500 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

Concentration1.5 mg/mL
BufferpH: 7.5 / Component:
ConcentrationNameFormula
5.0 mMHEPES
75.0 mMNaCl
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL 3200FSC
TemperatureMin: 85.0 K / Max: 85.0 K
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 271 / Average exposure time: 8.0 sec. / Average electron dose: 72.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 1.8 µm / Calibrated defocus min: 0.6 µm / Calibrated magnification: 44642 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.2 mm / Nominal magnification: 30000
Sample stageSpecimen holder model: JEOL / Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware - Name: Gctf (ver. 1.06)
Startup modelType of model: EMDB MAP
EMDB ID:

9599


Details: the map was filtered to 10 angstrom resolution
Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 184777
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
FSC plot (resolution estimation)

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