EMPIAR-10347 - FAK structure from single particle analysis of 2D crystals [multiple data sets in MRC, TIFF and MRCS formats]

EMPIAR-10347

FAK structure from single particle analysis of 2D crystals [multiple data sets in MRC, TIFF and MRCS formats]

Publication:

Structural basis of Focal Adhesion Kinase activation on lipid membranes

Acebrón I, Righetto RD, Schoenherr C, de Buhr S, Redondo P, Culley J, Rodríguez CF, Daday C, Biyani N, Llorca O, Byron A, Chami M, Gräter F, Boskovic J, Frame MC, Stahlberg H, Lietha D

The EMBO journal (2020)

PMID: 32779739

DOI: 10.15252/embj.2020104743

Related EMDB entry:

EMD-10616 EMD-10615

Deposited:

2020-01-16

Released:

2020-08-25

Last modified:

2020-08-25

Imageset size:

1.79 TB

Imageset DOI:

10.6019/EMPIAR-10347

Experimental metadata:

Download xml json

Contains:

micrographs - single frame
micrographs - multiframe
picked particles - single frame - unprocessed

Image Sets

1. Dose-weighted aligned movie averages of the FAK AMP-PNP dataset

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

2513

Image size:

(3838, 3710)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.058, 1.058)

Details:

The filenames contain the tilt angle estimated by FOCUS as well as their unique ID within the FOCUS project.
Micrographs have been downsampled by a factor of two in relation to the super-resolution movies, i.e. they are at the physical pixel size.
More details in the data/README file.

Files:

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Depending on the number and size of files to be downloaded, this can take an enormous amount of time. Also, this feature is unstable and may not work properly, and checksums of downloaded files are not verified.

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

2. Unaligned movies of the FAK AMP-PNP dataset

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

2513

Image size:

(7676, 7420)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.529, 0.529)

Details:

Movies have been acquired in super-resolution mode of the K2 detector.
The gain reference and defects list file are stored under data/amp-pnp/micrographs/gainref/.
The filenames contain the tilt angle estimated by FOCUS as well as their unique ID within the FOCUS project.
More details in the data/README file.

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. Stack of particles extracted from the FAK AMP-PNP dataset

Category:

picked particles - single frame - unprocessed

Image format:

MRCS

No. of images or tilt series:

2666154

Image size:

(200, 200)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(2.116, 2.116)

Details:

Particle boxes have been downsampled by a factor of two in relation to the aligned micrographs.
The initial orientations and defocii values are determined from the 2D crystal processing are available in the particles.star file.
More details in the data/README file.

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)

4. Dose-weighted aligned movie averages of the FAK APO Polara dataset

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

Image size:

(3808, 3808)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.7, 1.7)

Details:

The filenames contain the tilt angle estimated by FOCUS as well as their unique ID within the FOCUS project.
More details in the data/README file.

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)

5. Dose-weighted aligned movie averages of the FAK APO Titan dataset

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

509

Image size:

(3808, 3808)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.058, 1.058)

Details:

The filenames contain the tilt angle estimated by FOCUS as well as their unique ID within the FOCUS project.
More details in the data/README file.

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)

6. Unaligned movies of the FAK APO Titan dataset

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

509

Image size:

(7676, 7420)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.529, 0.529)

Details:

Movies have been acquired in super-resolution mode of the K2 detector.
The gain reference and defects list file are stored under data/apo/micrographs/titan/gainref/.
The filenames contain the tilt angle estimated by FOCUS as well as their unique ID within the FOCUS project.
More details in the data/README file.

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)

7. Stack of particles extracted from the FAK APO Titan and Polara datasets

Category:

picked particles - single frame - unprocessed

Image format:

MRCS

No. of images or tilt series:

361796

Image size:

(238, 238)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.7, 1.7)

Details:

Particle boxes extracted from the Titan dataset have been downsampled to approximately match the pixel size of the Polara dataset. The stack contains all particles extracted from the FAK APO Titan and Polara datasets merged.
The initial orientations and defocii values are determined from the 2D crystal processing are available in the particles_preprocessed.star file.
More details in the data/README file.

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)

Browse All Files

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