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- EMDB-41257: Purified arrayed human chromatin -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-41257
TitlePurified arrayed human chromatin
Map dataPurified Arrayed Human Chromatin (Weighted Backprojection)
Sample
  • Complex: Purified Arrayed Human Chromatin
KeywordsChromatin / Tomogram / denoise / segmentation / DNA
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM
AuthorsSwulius MT
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) United States
CitationJournal: To be Published
Title: Rapid Synthesis of Cryo-ET Data for Training Deep Learning Models.
Authors: Purnell C / Heebner J / Hylton RH / Kabonick S / Grillo M / Grigoryev S / Heberle F / Waxham NM / Swulius MT
History
DepositionJul 15, 2023-
Header (metadata) releaseJul 17, 2024-
Map releaseJul 17, 2024-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41257.png

Downloads & links

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Map

FileDownload / File: emd_41257.map.gz / Format: CCP4 / Size: 142 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationPurified Arrayed Human Chromatin (Weighted Backprojection)
Voxel sizeX=Y=Z: 6.6 Å
Density
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)1.498501 (±24.969908)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin003
Dimensions14401024101
Spacing10241440101
CellA: 6758.4 Å / B: 9504.0 Å / C: 666.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Purified Arrayed Human Chromatin (Regression Denoised)

Fileemd_41257_additional_1.map
AnnotationPurified Arrayed Human Chromatin (Regression Denoised)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Purified Arrayed Human Chromatin (Greyscale Segmentation)

Fileemd_41257_additional_2.map
AnnotationPurified Arrayed Human Chromatin (Greyscale Segmentation)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Purified Arrayed Human Chromatin

EntireName: Purified Arrayed Human Chromatin
Components
  • Complex: Purified Arrayed Human Chromatin

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Supramolecule #1: Purified Arrayed Human Chromatin

SupramoleculeName: Purified Arrayed Human Chromatin / type: complex / ID: 1 / Parent: 0
Details: Weighted Backprojection, Regression Denoised, and Greyscale Segmentation
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Ted Pella / Diameter: 10 nm

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 5.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 6.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 24

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