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:

354.23 GB

Imageset DOI:

10.6019/EMPIAR-10097

Experimental metadata:

Download xml json

Compressed by PDBj:

Image formats and pixel types shown below are those of the original, non-compressed files.

MRC movies (data/Raw-Frames/*.frames.mrc) in this entry were compressed by bzip2 (pbzip2)
by EMPIAR Japan to save space and bandwidth.

Some programs (e.g. RELION >= 4.0.1 and CryoSPARC) can process compressed movies without explicit
decompression. For other programs, movies have to be decompressed beforehand. In this case,
you might want to convert decompressed MRC movies into TIFF to save your local storage.

Original size:   1,857,743,258 kilobytes
Compressed size:   300,619,917 kilobytes

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.

rsync -av --files-from=(path-to-filelist) rsync://empiar.pdbj.org/empiar/archive (path-to-destination)

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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Yu C, Xu Z, Zeng Q, Wan X, El-Messiry H, Zhang F, Han R. (2026)

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Poudel B, Gyawali R, Dhakal A, Cheng J, Xu D. (2026)

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Deng Y, Wang S, Xiang M, Li Y, Zhuo L, Cao D, Fu X, Zou Q. (2026)

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He L, Bartesaghi A. (2026)

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

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