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- EMDB-75263: Apoferritin single-particle cryo-EM reconstruction using a Volta ... -

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Basic information

Entry
Database: EMDB / ID: EMD-75263
TitleApoferritin single-particle cryo-EM reconstruction using a Volta phase plate
Map data
Sample
  • Complex: Comparative apoferritin single-particle cryo-EM acquired with a Volta phase plate
Keywordsapoferritin / ferritin / iron storage / protein nanocage / METAL BINDING PROTEIN
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.9 Å
AuthorsYu Y / Montabana L
Funding support United States, 1 items
OrganizationGrant numberCountry
Chan Zuckerberg Initiative United States
CitationJournal: To Be Published
Title: Evaluating the Volta Phase Plate for Improved Tomogram Alignment in Cryo-Electron Tomography
Authors: Yu Y
History
DepositionJan 26, 2026-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75263.png

Downloads & links

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Map

FileDownload / File: emd_75263.map.gz / Format: CCP4 / Size: 1.6 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.29 Å/pix.
x 760 pix.
= 218.88 Å		0.29 Å/pix.
x 760 pix.
= 218.88 Å		0.29 Å/pix.
x 760 pix.
= 218.88 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.288 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.103
Minimum - Maximum-0.20018142 - 0.42716855
Average (Standard dev.)-0.000059485803 (±0.017666267)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions760760760
Spacing760760760
CellA=B=C: 218.87999 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_75263_msk_1.map
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Half map: #1

Fileemd_75263_half_map_1.map
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Half map: #2

Fileemd_75263_half_map_2.map
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Sample components

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Entire : Comparative apoferritin single-particle cryo-EM acquired with a V...

EntireName: Comparative apoferritin single-particle cryo-EM acquired with a Volta phase plate
Components
  • Complex: Comparative apoferritin single-particle cryo-EM acquired with a Volta phase plate

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Supramolecule #1: Comparative apoferritin single-particle cryo-EM acquired with a V...

SupramoleculeName: Comparative apoferritin single-particle cryo-EM acquired with a Volta phase plate
type: complex / ID: 1 / Parent: 0
Details: This map is a single-particle cryo-EM reconstruction of apoferritin acquired using a Volta phase plate with low defocus under matched sample preparation and processing conditions. Using the ...Details: This map is a single-particle cryo-EM reconstruction of apoferritin acquired using a Volta phase plate with low defocus under matched sample preparation and processing conditions. Using the same number of particles (300,702), the final reconstruction reached a global resolution of 1.90 angstrom.
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

Concentration19 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: O (octahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 1.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 300702
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 1 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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