EMPIAR-11618 - Single-particle cryo-EM dataset of an asymmetric nucleosome (10-N-0) [multiple data sets in TIFF and MRCS formats]

EMPIAR-11618

Single-particle cryo-EM dataset of an asymmetric nucleosome (10-N-0) [multiple data sets in TIFF and MRCS formats]

Publication:

Structure and dynamics of the chromatin remodeler ALC1 bound to a PARylated nucleosome

Gaullier G, Sabantsev A, Lehmann LC, Brackmann K, Dimakou D, Halic M, Hewitt G, Boulton SJ, Deindl S

eLife 10 (2021)

PMID: 34486521

DOI: 10.7554/elife.71420

Related EMDB entry:

EMD-17944

Deposited:

2023-07-05

Released:

2023-08-25

Last modified:

2024-08-29

Imageset size:

1.15 TB

Imageset DOI:

10.6019/EMPIAR-11618

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe
picked particles - single frame - processed

Image Sets

1. Unaligned movies

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

1537

Image size:

(4096, 4096)

Pixel type:

SIGNED 16 BIT INTEGER

Pixel spacing:

(0.952, 0.952)

Details:

The pixel size of 0.9783 A/pix in the tiff header is wrong, the correct one is 0.952 as indicated in the deposition metadata. This discrepancy comes from the fact that this dataset was collected during commissioning of the microscope, before the pixel size at this magnification was calibrated.

The coordinates deposited here are the particles that gave the reconstruction deposited as EMD-17944.

Files:

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

2. Extracted particles

Category:

picked particles - single frame - processed

Image format:

MRCS

No. of images or tilt series:

68401

Image size:

(256, 256)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(0.952, 0.952)

Details:

Particle stack extracted from motion-corrected micrographs. Running ab initio reconstruction and 3D refinement on them should reproduce the reconstruction deposited as EMD-17944.

Files:

選択したファイルを無圧縮zipファイルにアーカイブ化してダウンロードします。

rsync、aspera、globus 等の利用をおすすめします。

選択したファイルのリストをダウンロードします。

rsyncコマンド等でファイルリストを指定してダウンロードすることが可能です。

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

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Citations

A variational framework with composite sparse regularization for cryo-electron tomography reconstruction.

Yu C, Xu Z, Zeng Q, Wan X, El-Messiry H, Zhang F, Han R. (2026)

CryoFSL: an annotation-efficient, few-shot learning framework for robust protein particle picking in cryo-electron microscopy micrographs.

Poudel B, Gyawali R, Dhakal A, Cheng J, Xu D. (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)

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

He L, Bartesaghi A. (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)

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

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

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

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

See all citations

Protein Data Bank Japan News

[2026-06-10]

333件のPDBエントリーが新たに公開されました。（2026-06-10付）