EMPIAR-10097 - 40 Degree Tilted Single-Particle CryoEM of Highly Preferred Orientated Influenza Hemagglutinin Trimer [multiple data sets in MRC format]

EMPIAR-10097

40 Degree Tilted Single-Particle CryoEM of Highly Preferred Orientated Influenza Hemagglutinin Trimer [multiple data sets in MRC format]

Publication:

Addressing preferred specimen orientation in single-particle cryo-EM through tilting

Tan YZ, Baldwin PR, Davis JH, Williamson JR, Potter CS, Carragher B, Lyumkis D

Nature methods 14 (2017) 793-796

PMID: 28671674

DOI: 10.1038/nmeth.4347

Related EMDB entry:

EMD-8731

Deposited:

2017-05-11

Released:

2017-08-16

Last modified:

2021-11-02

Imageset size:

1.97 TB

Imageset DOI:

10.6019/EMPIAR-10097

Experimental metadata:

Download xml json

Contains:

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

Image Sets

1. Unaligned raw multi-frame 40 degree tilted micrographs of Influenza Hemagglutinin Trimer

Category:

micrographs - multiframe

Image format:

MRC

No. of images or tilt series:

668

Image size:

(3838, 3710)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.31, 1.31)

Details:

Unaligned raw multi-frame 40 degree tilted micrographs of Influenza Hemagglutinin Trimer. Micrographs were collected when tilt angle is set to -40 degrees. The gain normalization reference images (bright and norm) are included for each of the 3 sessions. No dark gain reference images are present because dark images values are always zero in counting mode camera.

Files:

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2. Aligned, summed and exposure weighted 40 degree tilted micrographs of Influenza Hemagglutinin Trimer

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

668

Image size:

(3838, 3710)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.31, 1.31)

Details:

Aligned, summed and exposure weighted 40 degree tilted micrographs of Influenza Hemagglutinin Trimer. Micrographs were aligned and summed from the raw frames using MotionCor2, with 5 by 5 patch and exposure weighting.

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.

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3. Equalized particle stack of Influenza Hemagglutinin Trimer from 40 degree tilted micrographs

Category:

picked particles - multiframe - processed

Image format:

MRC

No. of images or tilt series:

130000

Image size:

(256, 256)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.31, 1.31)

Details:

Equalized particle stack of Influenza Hemagglutinin Trimer from 40 degree tilted micrographs. Particles were extracted from aligned, exposured weighted and summed micrographs. In order to compare these particles with a 40 degree tilted dataset, these particles were equalized based on GCTF-estimated per-particle CTF values so a subset of particles with the same defocus spread would be obtained. This equalized stack of 130,000 is the uploaded stack. A Relion .star metadata file is also provided containing the final refined Euler angles.

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

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

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

Laser flash melting cryo-EM samples to overcome preferred orientation.

Straub MS, Harder OF, Mowry NJ, Barrass SV, Hruby J, Drabbels M, Lorenz UJ. (2025)

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Liu HF, Zhou Y, Huang Q, Martin J, Bartesaghi A. (2025)

CryoPROS: Correcting misalignment caused by preferred orientation using AI-generated auxiliary particles.

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Few-shot learning for non-vitrified ice segmentation.

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Automated removal of corrupted tilts in cryo-electron tomography.

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Probabilistic single-particle cryo-EM ab initio 3D reconstruction in SIMPLE.

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