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- EMDB-14333: 64K super-resolution CDS Apoferritin map -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-14333
Title64K super-resolution CDS Apoferritin map
Map dataRelion post processed map
Sample
  • Complex: human Apoferritin
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.87 Å
AuthorsClare DK
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Not fundedcm26464-2 United Kingdom
CitationJournal: To Be Published
Title: 1.87 A STRUCTURE OF HUMAN APOFERRITIN OBTAINED FROM TITAN KRIOS 2 AT eBIC, DLS UNDER COMMISSIONING SESSION CM26464-2
Authors: Clare DK
History
DepositionFeb 11, 2022-
Header (metadata) releaseFeb 22, 2023-
Map releaseFeb 22, 2023-
UpdateFeb 22, 2023-
Current statusFeb 22, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14333.png

Downloads & links

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Map

FileDownload / File: emd_14333.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRelion post processed map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.68 Å/pix.
x 400 pix.
= 271.2 Å		0.68 Å/pix.
x 400 pix.
= 271.2 Å		0.68 Å/pix.
x 400 pix.
= 271.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.678 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.08659864 - 0.21664283
Average (Standard dev.)0.00018602895 (±0.0060406076)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 271.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map

Fileemd_14333_half_map_1.map
AnnotationHalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map

Fileemd_14333_half_map_2.map
AnnotationHalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : human Apoferritin

EntireName: human Apoferritin
Components
  • Complex: human Apoferritin

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Supramolecule #1: human Apoferritin

SupramoleculeName: human Apoferritin / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1 / Details: Heavy chain
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 500 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

Concentration0.01 mg/mL
BufferpH: 7.5 / Details: 50 mM Tris-HCl, pH 7.5, 100 mM NaCl, 1 mM TCEP
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot time of 2.5 seconds.
DetailsThe apoferritin sample was applied to in-house graphene-coated Quantifoil r2/2 EM grid

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 11520 pixel / Digitization - Dimensions - Height: 8184 pixel / Number grids imaged: 1 / Number real images: 450 / Average exposure time: 8.0 sec. / Average electron dose: 33.6 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: 0.9 µm / Nominal magnification: 64000
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

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: O (octahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 1.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 320000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7r5o

RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient

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