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- EMDB-48840: Apoferritin (Experiment 1 Counted Super-resolution bin 2 accurate... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-48840
TitleApoferritin (Experiment 1 Counted Super-resolution bin 2 accurate TIFF)
Map dataExperiment 1 VitroEase Apoferritin Standard. Data collected in Counted Super resolution, Accurate mode with Binning 2 and saved as Tiff.
Sample
  • Complex: VitroEase Apoferritin Standard protein
KeywordsMETAL BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.14 Å
AuthorsLiu B / Kompaniiets D / Ajit KS / Bhandari J
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: BMC Methods / Year: 2025
Title: Efficient strategies and troubleshooting for single particle cryoEM data collection using EPU
Authors: Bhandari J / Kompaniiets D / Singh AK / Bator C / Porta J / Liu B
History
DepositionJan 29, 2025-
Header (metadata) releaseFeb 19, 2025-
Map releaseFeb 19, 2025-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48840.png

Downloads & links

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Map

FileDownload / File: emd_48840.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationExperiment 1 VitroEase Apoferritin Standard. Data collected in Counted Super resolution, Accurate mode with Binning 2 and saved as Tiff.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 336 pix.
= 223.104 Å		0.66 Å/pix.
x 336 pix.
= 223.104 Å		0.66 Å/pix.
x 336 pix.
= 223.104 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.664 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.238
Minimum - Maximum-0.6054474 - 1.0013983
Average (Standard dev.)0.00026766182 (±0.058523007)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 223.10399 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_48840_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 B

Fileemd_48840_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : VitroEase Apoferritin Standard protein

EntireName: VitroEase Apoferritin Standard protein
Components
  • Complex: VitroEase Apoferritin Standard protein

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Supramolecule #1: VitroEase Apoferritin Standard protein

SupramoleculeName: VitroEase Apoferritin Standard protein / type: complex / ID: 1 / Parent: 0
Details: VitroEase Apoferritin Standard protein, purchased from Thermo Fisher Scientific,
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 474 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

Concentration3.5 mg/mL
BufferpH: 7
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Digitization - Dimensions - Width: 4092 pixel / Digitization - Dimensions - Height: 5760 pixel / Number grids imaged: 1 / Number real images: 1354 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 130000
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

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 2.14 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 167034
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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