EMPIAR-12387 - Vibrio cholerae DdmD apo complex [multiple data sets in TIFF and MRC formats]

EMPIAR-12387

Vibrio cholerae DdmD apo complex [multiple data sets in TIFF and MRC formats]

Publication:

Molecular mechanism of plasmid elimination by the DdmDE defense system

Loeff L, Adams DW, Chanez C, Stutzmann S, Righi L, Blokesch M, Jinek M

Science (New York, N.Y.) 385 (2024) 188-194

PMID: 38870273

DOI: 10.1126/science.adq0534

Related EMDB entry:

EMD-50090

Deposited:

2024-10-29

Released:

2025-02-10

Last modified:

2025-02-10

Imageset size:

1.46 TB

Imageset DOI:

10.6019/EMPIAR-12387

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe
micrographs - single frame

Image Sets

1. Unaligned multi-frame micrographs of Vibrio cholerae DdmD apo complex

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

9026

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.65, 0.65)

Details:

The micrographs are 42 raw movie frames (accumulating 59.979 electrons per squared Angstrom in a 1.26 second exposure).

Files:

This entry cannot be downloaded from PDBj.

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

Depending on the number and size of files to be downloaded, this can take an enormous amount of time. Also, this feature is unstable and may not work properly, and checksums of downloaded files are not verified.

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)

2. Gain reference

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.65, 0.65)

Details:

---

Files:

This entry cannot be downloaded from PDBj.

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)

Browse All Files

Quick Links

Browse EMPIAR

Sample Preparation Widget

Volume Browser

Tomo Viewer Prototype

Claim entries to your ORCiD

Talks and Tutorials

EMPIAR Quick tour

Publications

Re-use study

Statistics

EMPIAR in the news

COVID-19 Data Portal

EMDB

BioImage Archive

PDBe

EMNavigator@PDBj

PDBj

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)

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)

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)

CryoSift: an accessible and automated CNN-driven tool for cryo-EM 2D class selection.

Schäfer JH, Calza A, Hom K, Damodar P, Peng R, Bogdanović N, Lander GC, Stagg SM, Cianfrocco MA. (2025)