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- EMDB-37173: Reprocessing of Fourier binned movies of EMPIAR-10216 Apoferritin... -

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Basic information

Entry
Database: EMDB / ID: EMD-37173
TitleReprocessing of Fourier binned movies of EMPIAR-10216 Apoferritin for PASR validation tests
Map dataPost-processed Fourier binned ApoF (EMPIAR 10216)
Sample
  • Complex: Apoferritin (mouse heavy chain)
KeywordsPASR / post-acquisition super resolution / apoferritin / reprocessing / METAL BINDING PROTEIN
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.068 Å
AuthorsBurton-Smith RN / Murata K
Funding support Japan, 1 items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
CitationJournal: To Be Published
Title: Reprocessing of Fourier binned movies of EMPIAR-10216 Apoferritin for PASR validation tests
Authors: Burton-Smith RN / Murata K
History
DepositionAug 13, 2023-
Header (metadata) releaseJan 17, 2024-
Map releaseJan 17, 2024-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37173.png

Downloads & links

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Map

FileDownload / File: emd_37173.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost-processed Fourier binned ApoF (EMPIAR 10216)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 200 pix.
= 206.8 Å		1.03 Å/pix.
x 200 pix.
= 206.8 Å		1.03 Å/pix.
x 200 pix.
= 206.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.034 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.075
Minimum - Maximum-0.1810083 - 0.32826602
Average (Standard dev.)0.000014637991 (±0.018720321)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 206.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half-map 1 Fourier binned ApoF (EMPIAR 10216)

Fileemd_37173_half_map_1.map
AnnotationHalf-map 1 Fourier binned ApoF (EMPIAR 10216)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2 Fourier binned ApoF (EMPIAR 10216)

Fileemd_37173_half_map_2.map
AnnotationHalf-map 2 Fourier binned ApoF (EMPIAR 10216)
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 (mouse heavy chain)

EntireName: Apoferritin (mouse heavy chain)
Components
  • Complex: Apoferritin (mouse heavy chain)

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Supramolecule #1: Apoferritin (mouse heavy chain)

SupramoleculeName: Apoferritin (mouse heavy chain) / 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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 50.0 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: 1.3 µm / Nominal defocus min: 0.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.068 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 149536
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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