EMPIAR-11844 - Cryo-EM of Tetrahymena ribozyme [multiple data sets in TIFF and MRC formats]

EMPIAR-11844

Cryo-EM of Tetrahymena ribozyme [multiple data sets in TIFF and MRC formats]

Publication:

Complex Water Networks Visualized through 2.2-2.3 Angstrom Cryogenic Electron Microscopy of RNA

Kretsch RC, Li S, Pintilie G, Palo MZ, Case DA, Das R, Zhang K, Chiu W

bioRxiv (2025)

DOI: 10.1101/2025.01.23.634578

Related EMDB entry:

EMD-42499 EMD-42498

Deposited:

2023-11-28

Released:

2025-02-04

Last modified:

2025-02-04

Imageset size:

3.65 TB

Imageset DOI:

10.6019/EMPIAR-11844

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe
picked particles - single frame - processed

Image Sets

1. Unaligned multi-frame micrographs of tetrahymena ribozyme.

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

18366

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.82, 0.82)

Details:

These micrographs were collected with a Titan Krios G3i, 300kV and a K3 detector. Over the collection, the sample was exposed evenly to 57.25 electrons per angstrom squared with a total exposure time of 2.5 seconds. Desired defocuses ranged from -0.5 to -2 nm. The exposures are not gain corrected, the gain reference can be found at data/ThR/exposures/K3-18210041 Gain Ref. x1.m1.mrc.

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2. Extracted particles and orientations for final reconstruction of tetrahymena ribozyme.

Category:

picked particles - single frame - processed

Image format:

MRC

No. of images or tilt series:

1181000

Image size:

(256, 256)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(0.82, 0.82)

Details:

Particles extracted from motion-corrected micrographs. The orientations for the final reconstruction can be found in data/ThR/particles/2.2A_cryosparc_P5_J1222_004_particles.cs and data/ThR/particles/2.3A_cryosparc_P5_J1224_004_particles.cs

Files:

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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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)