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- EMDB-36414: Apoferritin at 92% of super resolution sampling limit (200KV CRYO... -

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Basic information

Entry
Database: EMDB / ID: EMD-36414
TitleApoferritin at 92% of super resolution sampling limit (200KV CRYOARM + K3 with gold grids)
Map dataPostprocessed map: Apoferritin @ 92% of Super Resolution Nyquist limit (CRYOARM200 K3)
Sample
  • Complex: Apoferritin
KeywordsApoferritin / Benchmark / Super resolution / Sampling limit / METAL BINDING PROTEIN
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.93 Å
AuthorsBurton-Smith RN / Danev R / Murata K
Funding support Japan, 2 items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: To Be Published
Title: Apoferritin at 92% of super resolution sampling limit (200KV CRYOARM + K3 with gold grids)
Authors: Burton-Smith RN / Danev R / Murata K
History
DepositionJun 4, 2023-
Header (metadata) releaseJul 26, 2023-
Map releaseJul 26, 2023-
UpdateJul 26, 2023-
Current statusJul 26, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36414.png

Downloads & links

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Map

FileDownload / File: emd_36414.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed map: Apoferritin @ 92% of Super Resolution Nyquist limit (CRYOARM200 K3)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 320 pix.
= 283.36 Å		0.89 Å/pix.
x 320 pix.
= 283.36 Å		0.89 Å/pix.
x 320 pix.
= 283.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8855 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.103
Minimum - Maximum-0.38845915 - 0.6351581
Average (Standard dev.)0.000012385039 (±0.020528903)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 283.36002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 2: Apoferritin @ 92% of Super...

Fileemd_36414_half_map_1.map
AnnotationHalf map 2: Apoferritin @ 92% of Super Resolution Nyquist limit (CRYOARM200 K3)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1: Apoferritin @ 92% of Super...

Fileemd_36414_half_map_2.map
AnnotationHalf map 1: Apoferritin @ 92% of Super Resolution Nyquist limit (CRYOARM200 K3)
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

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: 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

BufferpH: 7
GridMaterial: GOLD / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 200
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.5 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.4 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 30000
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER

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Image processing

Startup modelType of model: INSILICO MODEL / In silico model: Ab initio model generated from dataset
Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 1.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 2268851
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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