EMPIAR-11987 - Single-particle cryo-EM dataset of the glycosyltransferase ArnC from Salmonella enterica in the UDP-bound state from Talos Arctica microscope [multiple data sets in TIFF and MRC formats]

EMPIAR-11987

Single-particle cryo-EM dataset of the glycosyltransferase ArnC from Salmonella enterica in the UDP-bound 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-43812

Deposited:

2024-02-27

Released:

2025-04-07

Last modified:

2025-04-07

Imageset size:

2.06 TB

Imageset DOI:

10.6019/EMPIAR-11987

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 UDP-bound state collected on Talos Arctica

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

7925

Image size:

(3838, 3710)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(0.818, 0.818)

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 165,000X, a nominal pixel size of 0.818 Å/pixel, and a dose rate of 5.0344 electrons/pixel/s. Movies were recorded at 100 ms/frame for 5.3s (53 frames total), resulting in a total dose of 39.88 electrons/Å2. Nominal defocus range was -0.5 to -2.5 μm. A total of 7,925 micrographs were recorded from one grid over two days. Micrographs were gain-normalized and defect corrected. At the end of processing a calibrated pixel size of 0.82 Å/pixel was determined for this dataset, representing an 0.24% error from the nominal pixel size value.

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

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

5556

Image size:

(3838, 3710)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(0.818, 0.818)

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 0.818 Å/pixel. Calibrated pixel size imposed on final reconstruction is 0.82 Å/pixel.

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3. Final particle stack of ArnC from S. enterica in the UDP-bound 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:

(0.818, 0.818)

Details:

Final particle stack of 216,104 particles from 5556 aligned/dose-weighted micrographs corresponding to the reconstruction deposited in EMD-43812. Nominal pixel size 0.818 Å/pixel. Calibrated pixel size imposed on final reconstruction is 0.82 Å/pixel.

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