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- EMDB-24099: Map of commercially purchased Apoferritin after 2 freeze-thaw cycles -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-24099
TitleMap of commercially purchased Apoferritin after 2 freeze-thaw cycles
Map data
Sample
  • Complex: Apoferritin
Biological speciesEquus ferus (tarpan)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.38 Å
AuthorsParvate AD / Moser TJ / Evans JE
Funding support United States, 1 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)FWP 74915 United States
CitationJournal: To Be Published
Title: Structure of commercially purchased Apoferritin after 2 freeze thaw cycles
Authors: Parvate AD / Moser TJ / Evans JE
History
DepositionMay 24, 2021-
Header (metadata) releaseJan 18, 2023-
Map releaseJan 18, 2023-
UpdateJan 18, 2023-
Current statusJan 18, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24099.png

Downloads & links

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Map

FileDownload / File: emd_24099.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.34 Å/pix.
x 400 pix.
= 135.92 Å		0.34 Å/pix.
x 400 pix.
= 135.92 Å		0.34 Å/pix.
x 400 pix.
= 135.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.3398 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.176161 - 2.3693922
Average (Standard dev.)-0.00030434242 (±0.08017933)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 135.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Apoferritin

EntireName: Apoferritin
Components
  • Complex: Apoferritin

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Supramolecule #1: Apoferritin

SupramoleculeName: Apoferritin / type: complex / ID: 1 / Parent: 0
Details: Commercially purchased fully assembled protein complex
Source (natural)Organism: Equus ferus (tarpan)
Molecular weightTheoretical: 444 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

Concentration10 mg/mL
BufferpH: 7
Details: Solutions made fresh and filtered with 0.22 micron filter for sterility.
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 295 K / Instrument: LEICA EM GP / Details: 2 s blot.
DetailsSample was monodisperse and suspended in TBS. Sample underwent 2 rounds of freeze thaw prior to plunge freezing

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsPhase plate: OTHER / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 1944 / Average exposure time: 1.56 sec. / Average electron dose: 50.13 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: -1.3 µm / Nominal defocus min: -0.3 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

DetailsImages collected in super resolution
Particle selectionNumber selected: 722538
Final reconstructionNumber classes used: 20 / Applied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 2.38 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.0) / Number images used: 539507
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 50 / Avg.num./class: 200 / Software - Name: cryoSPARC (ver. 300)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL

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