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- EMDB-28742: 1.42 Angstrom Apoferritin structure determined using G1 Titan kri... -

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Basic information

Entry
Database: EMDB / ID: EMD-28742
Title1.42 Angstrom Apoferritin structure determined using G1 Titan krios S-FEG operated at 300kV, zero loss imaging using Gatan BioQuantum energy filter operated at 10eV slit width and imaged using K2 camera.
Map dataSharpened map
Sample
  • Complex: Apoferritin
KeywordsApoferritin / METAL BINDING PROTEIN
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.42 Å
AuthorsVENUGOPAL H / RAMM G
Funding support Australia, 1 items
OrganizationGrant numberCountry
Australian Research Council (ARC)LE120100090 Australia
CitationJournal: To Be Published
Title: Apoferritin structure from G1 Titan krios S-FEG system operated at 300kV, zero loss imaging using BioQuantum energy filter operated at 10eV slit width and imaged using K2 camera.
Authors: Venugopal H / Ramm G
History
DepositionOct 31, 2022-
Header (metadata) releaseNov 23, 2022-
Map releaseNov 23, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28742.png

Downloads & links

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Map

FileDownload / File: emd_28742.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 360 pix.
= 234. Å		0.65 Å/pix.
x 360 pix.
= 234. Å		0.65 Å/pix.
x 360 pix.
= 234. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-1.6731958 - 4.391198
Average (Standard dev.)0.0021769856 (±0.12742297)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 233.99998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_28742_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

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Mask #2

Fileemd_28742_msk_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Additional map: Raw map

Fileemd_28742_additional_1.map
AnnotationRaw map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_28742_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_28742_half_map_2.map
Annotationhalf map 2
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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)
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

Concentration2 mg/mL
BufferpH: 8 / Details: 50 mM Tris-HCl (pH 8.0), 150 mM NaCl
GridModel: UltrAuFoil / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK III

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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 K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 3241 / Average electron dose: 60.0 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: 1.2 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 276084
Startup modelType of model: INSILICO MODEL
In silico model: generated using ab-initio reconstruction routine in cryoSPARC
Final reconstructionApplied symmetry - Point group: O (octahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 1.42 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 276084
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
FSC plot (resolution estimation)

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