EMPIAR-12002 - Single-particle cryo-EM dataset of the glycosyltransferase ArnC from Salmonella enterica in the apo state from Krios microscope [multiple data sets in TIFF and MRC formats]

EMPIAR-12002

Single-particle cryo-EM dataset of the glycosyltransferase ArnC from Salmonella enterica in the apo state from Krios 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-44302

Deposited:

2024-03-05

Released:

2025-06-02

Last modified:

2025-06-02

Imageset size:

5.92 TB

Imageset DOI:

10.6019/EMPIAR-12002

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 NCCAT Titan Krios #4 - "Elizabeth"

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

23259

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.646, 0.646)

Details:

The dataset contains unaligned non gain-corrected micrograph movies in TIFF format. Cryo-EM data were collected at the National Center for Cryo-EM Access and Training (NCCAT) using the 300kV Titan Krios #4 – “Elizabeth” (TFS) electron microscope, equipped with a K3 direct electron detector (Gatan) and a BioQuantum energy filter (Gatan) with slit width of 20 eV. Data were collected automatically in counting mode using image shift in Leginon, a nominal magnification of 130,000X, a nominal pixel size of 0.646 Å/pixel, and a dose rate of 19.9685 electrons/pixel/s. Movies were recorded at 30 ms/frame for 1.2s (40 frames total), resulting in a total dose of 57.42 electrons/Å2. Nominal defocus range was -0.8 to -2.0 μm. A total of 23,259 micrographs were recorded from one grid over three days. Micrographs were not gain-normalized or defect corrected. The gain reference is the file named "n21sep13b*norm_0.mrc" in the "references" folder. When importing into cryoSPARC the gain reference should be flipped in the Y axis. At the end of processing a calibrated pixel size of 0.67 Å/pixel was determined for this dataset, representing an 3.72% error from the nominal pixel size value.

Files:

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2. Aligned and dose-weighted micrographs of ArnC from S. enterica in the apo state collected on NCCAT Titan Krios #4 - "Elizabeth"

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

16451

Image size:

(5760, 4092)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(0.646, 0.646)

Details:

Aligned and dose-weighted micrographs produced from the raw movies using patch motion correction in cryoSPARC. The dataset contains a subset of micrographs that have contributed particles to the final particle stack. Nominal pixel size 0.646 Å/pixel. Calibrated pixel size imposed on final reconstruction is 0.67 Å/pixel.

Files:

This entry cannot be downloaded from PDBj.

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

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Download a list of selected files.

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3. Final particle stack of ArnC from S. enterica in the apo state collected on NCCAT Titan Krios #4 - "Elizabeth"

Category:

picked particles - single frame - processed

Image format:

MRC

No. of images or tilt series:

16451

Image size:

(480, 480)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(0.646, 0.646)

Details:

Final particle stack of 490,807 particles from 16,451 aligned/dose-weighted micrographs corresponding to the reconstruction deposited in EMD-44302. Nominal pixel size 0.646 Å/pixel. Calibrated pixel size imposed on final reconstruction is 0.67 Å/pixel. Box size of 480 px was used.

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)

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Citations

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He L, Bartesaghi A. (2026)

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

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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)

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

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

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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)