EMPIAR-11924 - Single-particle cryo-EM dataset of the glycosyltransferase ArnC from Salmonella enterica in the apo state from Talos Arctica microscope [multiple data sets in TIFF and MRC formats]

EMPIAR-11924

Single-particle cryo-EM dataset of the glycosyltransferase ArnC from Salmonella enterica in the apo state from Talos Arctica microscope [multiple data sets in TIFF and MRC formats]

Publication:

Structural basis of undecaprenyl phosphate glycosylation leading to polymyxin resistance in Gram-negative bacteria

Ashraf KU, Bunoro-Batista M, Ansell TB, Punetha A, Rosario-Garrido S, Firlar E, Kaelber JT, Stansfeld PJ, Petrou VI

bioRxiv (2025)

DOI: 10.1101/2025.01.29.634835

Related EMDB entry:

EMD-43617

Deposited:

2023-03-17

Released:

2025-06-13

Last modified:

2025-06-13

Imageset size:

1.30 TB

Imageset DOI:

10.6019/EMPIAR-11924

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe
micrographs - single frame
picked particles - single frame - processed

Image Sets

1. Unaligned multi-frame micrographs of ArnC from S. enterica in the apo state collected on Talos Arctica

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

5552

Image size:

(3838, 3710)

Pixel type:

UNSIGNED 32 BIT INTEGER

Pixel spacing:

(1.038, 1.038)

Details:

The dataset contains unaligned gain-corrected micrograph movies in TIFF format. Cryo-EM data were collected at the Rutgers Cryo-EM & Nanoimaging Facility using a 200 kV Talos Arctica (FEI/ThermoFisher) electron microscope equipped with a K2 Summit direct electron detector (Gatan) and a BioQuantum energy filter (Gatan) with slit width of 20 eV. Data were collected automatically in counting mode using EPU (FEI/ThermoFisher), a nominal magnification of 130,000X, a nominal pixel size of 1.038 Å/pixel, and a dose rate of 5.420 electrons/pixel/s. Movies were recorded at 200 ms/frame for 7s (35 frames total), resulting in a total radiation dose of 35.21 electrons/Å2. Nominal defocus range was -0.5 to -2.5 μm. A total of 5,552 micrographs were recorded from one grid over three days. Micrographs were gain-normalized and defect corrected. At the end of processing a calibrated pixel size of 1.05 Å/pixel was determined for this dataset, representing an 1.16% error from the nominal pixel size value.

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. Aligned and dose-weighted micrographs of ArnC from S. enterica in the apo state collected on Talos Arctica

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

3318

Image size:

(3838, 3710)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.038, 1.038)

Details:

Aligned and dose-weighted micrographs produced from the raw movies using patch motion correction in cryoSPARC. This dataset only contains a subset of micrographs that have contributed particles to the final particle stack. Nominal pixel size 1.038 Å/pixel. Calibrated pixel size imposed on final reconstruction is 1.05 Å/pixel.

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)

3. Final particle stack of ArnC from S. enterica in the apo state collected on Talos Arctica

Category:

picked particles - single frame - processed

Image format:

MRC

No. of images or tilt series:

3318

Image size:

(288, 288)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.038, 1.038)

Details:

Final particle stack of 184,679 from 3318 aligned/dose-weighted micrographs corresponding to the reconstruction deposited in EMD-43617. Nominal pixel size 1.038 Å/pixel. Calibrated pixel size imposed on final reconstruction is 1.05 Å/pixel.

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)

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)