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- EMDB-41933: CryoEM map of horse spleen apoferritin determined as a reference ... -

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Basic information

Entry
Database: EMDB / ID: EMD-41933
TitleCryoEM map of horse spleen apoferritin determined as a reference for benchmarking square and rectangular apertures for cryo-EM
Map dataMain map, Gatan K3 dataset using standard round beam (50 micron aperture) for comparison with square and rectangular aperture results. Sharpened with B-factor of 52.6.
Sample
  • Complex: Apoferritin from equine spleen
    • Protein or peptide: Apoferritin from equine spleen
KeywordsApo-ferritin / METAL BINDING PROTEIN
Biological speciesEquus caballus (horse)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.81 Å
AuthorsBrown HG / Hanssen E
Funding support Australia, 1 items
OrganizationGrant numberCountry
Other governmentTA503491 Australia
CitationJournal: Nat Methods / Year: 2024
Title: Square condenser apertures for square cameras in low-dose transmission electron microscopy.
Authors: Hamish G Brown / Dan Smith / Benjamin C Wardle / Eric Hanssen /
Abstract: In transmission electron microscopy (TEM), cameras are square or rectangular but beams are round so the circular lobes irradiate adjacent areas, precluding further neighboring acquisition for beam- ...In transmission electron microscopy (TEM), cameras are square or rectangular but beams are round so the circular lobes irradiate adjacent areas, precluding further neighboring acquisition for beam-sensitive samples. We present condenser aperture plates with square and rectangular shapes that improve the efficiency of area usage by 70% and enhance montage imaging for beam-sensitive specimens. We demonstrate the compatibility of these condenser aperture plates with high-resolution cryogenic TEM by reconstructing a 1.8-Å map of equine apo-ferritin.
History
DepositionSep 12, 2023-
Header (metadata) releaseFeb 28, 2024-
Map releaseFeb 28, 2024-
UpdateApr 24, 2024-
Current statusApr 24, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41933.png

Downloads & links

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Map

FileDownload / File: emd_41933.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map, Gatan K3 dataset using standard round beam (50 micron aperture) for comparison with square and rectangular aperture results. Sharpened with B-factor of 52.6.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 460 pix.
= 301.3 Å		0.66 Å/pix.
x 460 pix.
= 301.3 Å		0.66 Å/pix.
x 460 pix.
= 301.3 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.655 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.54
Minimum - Maximum-1.2624726 - 2.1051235
Average (Standard dev.)-0.000041849118 (±0.06378621)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions460460460
Spacing460460460
CellA=B=C: 301.3 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41933_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_41933_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_41933_half_map_2.map
AnnotationHalf 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 : Apoferritin from equine spleen

EntireName: Apoferritin from equine spleen
Components
  • Complex: Apoferritin from equine spleen
    • Protein or peptide: Apoferritin from equine spleen

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Supramolecule #1: Apoferritin from equine spleen

SupramoleculeName: Apoferritin from equine spleen / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Purchased from Sigma Aldrich product number A3641
Source (natural)Organism: Equus caballus (horse)
Molecular weightTheoretical: 481.2 KDa

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Macromolecule #1: Apoferritin from equine spleen

MacromoleculeName: Apoferritin from equine spleen / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Equus caballus (horse)
SequenceString:
SQIRQNYSTE VEAAVNRLV N LYLRASYT YL SLGFYFD RDD VALEGV CHFF RELAE EKREG AERL LKMQNQ RGG RALFQDL QK PSQDEWGT T LDAMKAAIV LEKSLNQALL DLHALGSAQ A DPHLCDFL ES HFLDEEV KLI KKMGDH LTNI QRLVG SQAGL GEYL FERLTL K

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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

Concentration35 mg/mL
BufferpH: 7.4 / Component - Formula: PBS
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 180 sec. / Pretreatment - Atmosphere: AIR / Details: Quorum Glocube
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV
DetailsSolution purchased from Sigma Aldrich and no further purification

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 3111 / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 346411
Startup modelType of model: OTHER / Details: Ab-initio model
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 1.81 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3.1) / Number images used: 346411
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.1) / Details: Homogeneous Refinement
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.1) / Details: Homogeneous Refinement
Final 3D classificationNumber classes: 50 / Avg.num./class: 7700 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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