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- EMDB-77042: Apoferritin with crossed laser phase plate (xLPP), xLPP-on -

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Basic information

Entry
Database: EMDB / ID: EMD-77042
TitleApoferritin with crossed laser phase plate (xLPP), xLPP-on
Map dataSharpened map
Sample
  • Complex: Mouse heavy chain apoferritin homo-24-mer
Keywordslaser phase plate / cryo-EM / benchmark / apoferritin / STRUCTURAL PROTEIN
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.79 Å
AuthorsYu Y / Kopylov M / Cheng A / Montabana E / Olshin P
Funding support United States, 1 items
OrganizationGrant numberCountry
Chan Zuckerberg Initiative United States
CitationJournal: To Be Published
Title: A Crossed Laser Phase Plate for Cryo-EM
Authors: Yu Y / Cheng A / Montabana E / Paz Soldan N / Cooper ES / Zhang JT / Axelrod JJ / Petrov PN / Torkaman A / Roof D / Derstine M / Buijsse B / Hagen W / Kimanius D / Zheng S / Kopylov M / ...Authors: Yu Y / Cheng A / Montabana E / Paz Soldan N / Cooper ES / Zhang JT / Axelrod JJ / Petrov PN / Torkaman A / Roof D / Derstine M / Buijsse B / Hagen W / Kimanius D / Zheng S / Kopylov M / Paraan M / Balakrishnan D / Cheng H / Remis J / Singh A / Maisenbacher L / Potter CS / Muller H / Carragher B / Agard D / Olshin PK
History
DepositionMay 4, 2026-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_77042.png

Downloads & links

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Map

FileDownload / File: emd_77042.map.gz / Format: CCP4 / Size: 347.6 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.)
0.7 Å/pix.
x 450 pix.
= 315.9 Å		0.7 Å/pix.
x 450 pix.
= 315.9 Å		0.7 Å/pix.
x 450 pix.
= 315.9 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.702 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.521
Minimum - Maximum-1.5776931 - 3.3888674
Average (Standard dev.)0.000040033454 (±0.08100272)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 315.90002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_77042_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_77042_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 A

Fileemd_77042_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mouse heavy chain apoferritin homo-24-mer

EntireName: Mouse heavy chain apoferritin homo-24-mer
Components
  • Complex: Mouse heavy chain apoferritin homo-24-mer

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Supramolecule #1: Mouse heavy chain apoferritin homo-24-mer

SupramoleculeName: Mouse heavy chain apoferritin homo-24-mer / type: complex / ID: 1 / Parent: 0
Details: Mouse heavy chain apoferritin purified in-house, stored at -80 degree C. Sample thawed on ice with 1 mM DTT added immediately before vitrification.
Source (natural)Organism: Mus musculus (house mouse)

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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: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsPhase plate: OTHER / Details: Imaged with a crossed laser phase plate
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.6 µm / Nominal defocus min: 0.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: cryoSPARC's ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.79 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 126270
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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