EMPIAR-13137 - Cryo electron ptychography of the Thermoplasma acidophilum 20S proteasome [multiple data sets in MRC format]

EMPIAR-13137

Cryo electron ptychography of the Thermoplasma acidophilum 20S proteasome [multiple data sets in MRC format]

Publication:

Sampling Mismatch and Correction for Ptychographic Single-Particle Analysis

Li T, Li S, Yan Z, Shen Y, Li X

(---)

Related EMDB entry:

EMD-67291 EMD-67292

Deposited:

2025-11-23

Released:

2025-12-22

Last modified:

2025-12-22

Imageset size:

1.84 TB

Imageset DOI:

10.6019/EMPIAR-13137

Experimental metadata:

Download xml json

Contains:

diffraction images

Image Sets

1. Diffraction images of T20S proteasome

Category:

diffraction images

Image format:

MRC

No. of images or tilt series:

222

Image size:

(None, None)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(None, None)

Details:

These are the convergent beam electron diffraction (CBED) images of T20S proteasome in EMPAD G1 data format (.raw). Each set of CBED images corresponds to one ptychographic micrograph. Key parameters of each set of CBED images are listed below:
1. Acceleration voltage: 300 kV
2. Convergence semi-angle: ~ 3.69 mrad
3. Defocus: ~ 1.0-2.0 μm
4. Scanning step size: 10.20 Å (nominal value: 11.20 Å)
5. STEM array: 300 × 300
6. CBED image pixel size: 0.005570 1/Å
7. Number of CBED image pixels: 128 × 128

Files:

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2. Diffraction images of T20S proteasome

Category:

diffraction images

Image format:

MRC

No. of images or tilt series:

166

Image size:

(None, None)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(None, None)

Details:

These are the convergent beam electron diffraction (CBED) images of T20S proteasome in EMPAD G1 data format (.raw). Each set of CBED images corresponds to one ptychographic micrograph. Key parameters of each set of CBED images are listed below:
1. Acceleration voltage: 300 kV
2. Convergence semi-angle: ~ 3.69 mrad
3. Defocus: ~ 1.0-2.0 μm
4. Scanning step size: 12.25 Å (nominal value: 13.44 Å)
5. STEM array: 250 × 250
6. CBED image pixel size: 0.005570 1/Å
7. Number of CBED image pixels: 128 × 128

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

GTpick: A deep neural network for Cryo-EM particle detection.

Ni S, Yang C, Liu Y, Zhang Y, Shi Y, Qian A, Kong R, Chang S. (2025)

High-resolution ab initio reconstruction enables cryo-EM structure determination of small particles

Kim K, Li H, Clarke OB. (2025)

CLEM-Reg: an automated point cloud-based registration algorithm for volume correlative light and electron microscopy.

Krentzel D, Elphick M, Domart MC, Peddie CJ, Laine RF, Shand C, Henriques R, Collinson LM, Jones ML. (2025)

CryoEMNet driven symmetry-aware molecular reconstruction through deep learning enhanced electron microscopy.

Arora S, Pan SH, Kumar S, Singh SK, Chauhan U, Alhalabi W, Arya V, Alsulami BS, Hsu CH, Chui KT, Gupta BB. (2025)

PERC: a suite of software tools for the curation of cryoEM data with application to simulation, modeling and machine learning.

Costa-Gomes B, Greer J, Juraschko N, Parkhurst J, Mirecka J, Famili M, Rangel-Smith C, Strickson O, Lowe A, Basham M, Burnley T. (2025)

DiameTR: A cryo-EM tool for diameter sorting of tubular samples.

Peng R, Elkhaligy H, Grant T, Stagg SM. (2025)

Self-supervised learning for generalizable particle picking in cryo-EM micrographs.

Zamanos A, Koromilas P, Bouritsas G, Kastritis PL, Panagakis Y. (2025)

Localization of macromolecules in crowded cellular cryo-electron tomograms from extremely sparse labels.

Uddin MR, Ahmed AY, Tabib HMS, Tahmid MT, Alam MZU, Freyberg Z, Xu M. (2025)

Structural insight into bicarbonate-mediated carboxylation by human vitamin K-dependent carboxylase.

Wu K, Wang Z, Yao D, Li S, Wang X, Zhang Y, Cao M, Shen Y, Xing S, Wu J, Lei M, Lan P. (2025)

Conserved hydrophilic checkpoints tune FocA-mediated formate:H<sup>+</sup> symport.

Tüting C, Janson K, Kammel M, Ihling C, Lorenz J, Kyrilis FL, Hamdi F, Erdmann C, Sinz A, Sawers RG, Kastritis PL. (2025)

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