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- EMDB-36416: Apoferritin at 100% of super resolution sampling limit (Krios G4 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-36416
TitleApoferritin at 100% of super resolution sampling limit (Krios G4 + Falcon 4 with copper grids)
Map dataPostprocessed map: Apoferritin at super resolution sampling limit (Krios Falcon 4)(copper grid)
Sample
  • Complex: Apoferritin
KeywordsApoferritin / Benchmark / Super resolution / Sampling limit / METAL BINDING PROTEIN
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.91 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 100% of super resolution sampling limit (Krios G4 + Falcon 4 with copper 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_36416.png

Downloads & links

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Map

FileDownload / File: emd_36416.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed map: Apoferritin at super resolution sampling limit (Krios Falcon 4)(copper grid)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 220 pix.
= 210.32 Å		0.96 Å/pix.
x 220 pix.
= 210.32 Å		0.96 Å/pix.
x 220 pix.
= 210.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.956 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.18882126 - 0.4182693
Average (Standard dev.)-0.000008752442 (±0.018754844)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 210.31999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 1: Apoferritin at super resolution sampling...

Fileemd_36416_half_map_1.map
AnnotationHalf map 1: Apoferritin at super resolution sampling limit (Krios Falcon 4)(copper grid)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2: Apoferritin at super resolution sampling...

Fileemd_36416_half_map_2.map
AnnotationHalf map 2: Apoferritin at super resolution sampling limit (Krios Falcon 4)(copper grid)
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: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL / In silico model: Ab initio model generated from data
Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 1.91 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 2416769
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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