EMPIAR-12572 - Cryo electron micrographs of Arabidopsis thaliana H2A.Z-H3.3-nucleosome with Arabidopsis native 147bp DNA 15.2.2 [multiple data sets in TIFF, MRC and MRCS formats]

EMPIAR-12572

Cryo electron micrographs of Arabidopsis thaliana H2A.Z-H3.3-nucleosome with Arabidopsis native 147bp DNA 15.2.2 [multiple data sets in TIFF, MRC and MRCS formats]

Publication:

unpublished

Wang Y

(---)

Related EMDB entry:

EMD-62046 EMD-62045

Deposited:

2025-02-14

Released:

2025-12-07

Last modified:

2025-12-07

Imageset size:

1.95 TB

Imageset DOI:

10.6019/EMPIAR-12572

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe
micrographs - single frame
picked particles - single frame - unprocessed

Image Sets

1. Cryo electron micrographs of Arabidopsis thaliana H2A.Z-H3.3-nucleosome with Arabidopsis native 147bp DNA 15.2.2

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

3802

Image size:

(11520, 8184)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(1.1, 1.1)

Details:

---

Files:

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2. Gain reference for cryo electron micrographs of Arabidopsis thaliana H2A.Z-H3.3-nucleosome with Arabidopsis native 147bp DNA 15.2.2

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

Image size:

(11520, 8184)

Pixel type:

16 BIT FLOAT

Pixel spacing:

(1.1, 1.1)

Details:

This gain reference doesn't need rotation and flipping.

Files:

Archives and downloads the selected files into an uncompressed zip file.

We recommend using rsync, aspera, globus, etc.

Download a list of selected files.

It is possible to download files by specifying the file list with rsync command, etc.

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3. Particles for cryo electron micrographs of Arabidopsis thaliana H2A.Z-H3.3-nucleosome with Arabidopsis native 147bp DNA 15.2.2

Category:

picked particles - single frame - unprocessed

Image format:

MRCS

No. of images or tilt series:

2942

Image size:

(256, 256)

Pixel type:

16 BIT FLOAT

Pixel spacing:

(1.1, 1.1)

Details:

The folder cryosparc/J1 is "Imported particles" of CryoSPARC-v4.3.1, and the particles is imported from "Particle extraction" of relion-v3.1.3.
The folder cryosparc/J7 is "Homogeneous Refinement" of CryoSPARC-v4.3.1, and this "Homogeneous Refinement" which imposed C1 symmetry is at a resolution of 2.90 angstrom.
The folder cryosparc/J15 is "Homogeneous Refinement" of CryoSPARC-v4.3.1, and this "Homogeneous Refinement" which imposed C2 symmetry is at a resolution of 2.71 angstrom.

Files:

Archives and downloads the selected files into an uncompressed zip file.

We recommend using rsync, aspera, globus, etc.

Download a list of selected files.

It is possible to download files by specifying the file list with rsync command, etc.

rsync -av --files-from=(path-to-filelist) rsync://empiar.pdbj.org/empiar/archive (path-to-destination)

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Citations

prismPYP: Power-spectrum and image domain learning for self-supervised micrograph evaluation.

He L, Bartesaghi A. (2026)

CryoSIP: unleashing protein high-resolution Cryo-EM via semantic-instance collaborative picking.

Deng Y, Wang S, Xiang M, Li Y, Zhuo L, Cao D, Fu X, Zou Q. (2026)

Unbend, correction of local beam-induced sample motion in cryo-EM images using a 3D spline model.

Kong L, Zottig X, Elferich J, Grigorieff N. (2026)

Chart builder: an interactive tool for user driven data visualization in the electron microscopy data bank.

Fonseca N, Duraisamy AK, Wang Z, Somasundharam S, Tayebinia M, de Oliveira LC, Ma M, Turner J, Patwardhan A, Kleywegt GJ, Hartley M, Morris KL. (2026)

Dual site targeting of the bacterial 70S ribosome by tetracyclines.

Devarkar SC, Lomakin IB, Wang J, Grada A, Bunick CG. (2026)

CryoVirusDB: An Annotated Dataset for AI-Based Virus Particle Identification in Cryo-EM Micrographs.

Gyawali R, Dhakal A, Wang L, Cheng J. (2026)

Deep-learning methods for contrast enhancement and artifact reduction in cryo-electron tomography: a systematic analysis of the state of the art and proposed improvements.

Jones HN, Deshmukh A, Pande K. (2026)

CryoGS: High-Quality Cryo-EM Homogeneous Reconstruction by Gaussian Splatting

Zeng B, Liu S, Cheng S, Xu G, Fan H. (2026)

Point cloud deformation modeling for particle selection following cryo-EM 2D classification.

Wang X, Mo Z, Li F, Zhang F, Wan X. (2026)

ICECREAM: high-fidelity equivariant cryo-electron tomography.

Kishore V, Debarnot V, Righetto RD, Engel BD, Dokmanić I. (2026)