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- EMDB-72191: Benchmarking Talos Arctica with K3 and Biocontinuum energy filter -

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Basic information

Entry
Database: EMDB / ID: EMD-72191
TitleBenchmarking Talos Arctica with K3 and Biocontinuum energy filter
Map data
Sample
  • Organelle or cellular component: Iron transport protein
    • Protein or peptide: ferritin heavy polypeptide 1
Keywordsbenchmarking microscope performance / METAL BINDING PROTEIN
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.88 Å
AuthorsMaruthi K / Morais M
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Benchmarking Talos Arctica with K3 and Biocontinuum energy filter
Authors: Maruthi K / Morais M
History
DepositionAug 18, 2025-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72191.png

Downloads & links

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Map

FileDownload / File: emd_72191.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 256 pix.
= 218.368 Å		0.85 Å/pix.
x 256 pix.
= 218.368 Å		0.85 Å/pix.
x 256 pix.
= 218.368 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.853 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.694
Minimum - Maximum-1.9055237 - 4.027122
Average (Standard dev.)0.0025087567 (±0.19114743)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 218.368 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72191_msk_1.map
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Mask #2

Fileemd_72191_msk_2.map
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Mask #3

Fileemd_72191_msk_3.map
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Half map: #2

Fileemd_72191_half_map_1.map
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Half map: #1

Fileemd_72191_half_map_2.map
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Sample components

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Entire : Iron transport protein

EntireName: Iron transport protein
Components
  • Organelle or cellular component: Iron transport protein
    • Protein or peptide: ferritin heavy polypeptide 1

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Supramolecule #1: Iron transport protein

SupramoleculeName: Iron transport protein / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all / Details: https://pubmed.ncbi.nlm.nih.gov/31078399/
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: ferritin heavy polypeptide 1

MacromoleculeName: ferritin heavy polypeptide 1 / type: protein_or_peptide / ID: 1 / Details: https://pubmed.ncbi.nlm.nih.gov/31078399/ / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MTTASPSQVR QNYHQDAEAA INRQINLELY ASYVYLSMSC YFDRDDVALK NFAKYFLHQS HEEREHAEKL MKLQNQRGGR IFLQDIKKPD RDDWESGLNA MECALHLEKS VNQSLLELHK LATDKNDPHL CDFIETYYLS EQVKSIKELG DHVTNLRKMG APEAGMAEYL FDKHTLGHGD ES

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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

Concentration8 mg/mL
BufferpH: 7.5
GridMaterial: GOLD
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Specialist opticsEnergy filter - Slit width: 20 eV / Details: GIF Biocontinuum
Detailsbeam-image shift data collection (8mrad)
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number grids imaged: 1 / Number real images: 1543 / Average exposure time: 2.0 sec. / Average electron dose: 43.81 e/Å2
Details: standard counting mode, beam image shift data collection
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.25 µm / Nominal magnification: 100000
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 909665
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Ab-initio
Final reconstructionNumber classes used: 8 / Applied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 1.88 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 647890
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 50 / Avg.num./class: 82000 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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