EMPIAR-10096 - Untilted Single-Particle CryoEM of Highly Preferred Orientated Influenza Hemagglutinin Trimer [multiple data sets in MRC format]

EMPIAR-10096

Untilted 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

Nature methods (2017)

PMID: 28671674

DOI: 10.1038/nmeth.4347

Related EMDB entry:

EMD-8731

Deposited:

2017-05-09

Released:

2017-05-15

Last modified:

2021-03-19

Imageset size:

247.49 GB

Imageset DOI:

10.6019/EMPIAR-10096

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:   1,243,130,593 kilobytes
Compressed size:   200,985,421 kilobytes

Contains:

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

Image Sets

1. Unaligned raw multi-frame untilted micrographs of Influenza Hemagglutinin Trimer

Category:

micrographs - multiframe

Image format:

MRC

No. of images or tilt series:

447

Image size:

(3838, 3710)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(1.31, 1.31)

Details:

Unaligned raw multi-frame untilted micrographs of Influenza Hemagglutinin Trimer. Micrographs were collected when tilt angle is set to zero. 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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選択したファイルのリストをダウンロードします。

rsyncコマンド等でファイルリストを指定してダウンロードすることが可能です。

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

2. Aligned, summed and exposure weighted untilted micrographs of Influenza Hemagglutinin Trimer

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

447

Image size:

(3838, 3710)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.31, 1.31)

Details:

Aligned, summed and exposure weighted untilted 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:

選択したファイルを無圧縮zipファイルにアーカイブ化してダウンロードします。

rsync、aspera、globus 等の利用をおすすめします。

選択したファイルのリストをダウンロードします。

rsyncコマンド等でファイルリストを指定してダウンロードすることが可能です。

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

3. Equalized particle stack of Influenza Hemagglutinin Trimer

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. 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:

選択したファイルを無圧縮zipファイルにアーカイブ化してダウンロードします。

rsync、aspera、globus 等の利用をおすすめします。

選択したファイルのリストをダウンロードします。

rsyncコマンド等でファイルリストを指定してダウンロードすることが可能です。

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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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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Protein Data Bank Japan News

[2026-06-10]

333件のPDBエントリーが新たに公開されました。（2026-06-10付）