EMPIAR-11058 - In situ cryo-electron tomography of T. kivui cells [multiple data sets in MRC and TIFF formats]

EMPIAR-11058

In situ cryo-electron tomography of T. kivui cells [multiple data sets in MRC and TIFF formats]

Publication:

Membrane-anchored HDCR nanowires drive hydrogen-powered CO₂ fixation

Dietrich HM, Righetto RD, Kumar A, Wietrzynski W, Trischler R, Schuller SK, Wagner J, Schwarz FM, Engel BD, Müller V, Schuller JM

Nature 607 (2022) 823-830

PMID: 35859174

DOI: 10.1038/s41586-022-04971-z

Related EMDB entry:

EMD-15053

Deposited:

2022-05-29

Released:

2022-07-12

Last modified:

2022-07-29

Imageset size:

373.37 GB

Imageset DOI:

10.6019/EMPIAR-11058

Experimental metadata:

Download xml json

Contains:

subtomograms
reconstructed volumes
tilt series
micrographs - multiframe

Image Sets

1. Subtomograms of HDCR filament particles at bin2

Category:

subtomograms

Image format:

MRC

No. of images or tilt series:

6727

Image size:

(96, 96)

Pixel type:

SIGNED BYTE

Pixel spacing:

(7.04, 7.04)

Details:

Particle coordinates and final orientations are given in file hdcr_tm_bin2_motl_12.star in STOPGAP format.

Files:

Archives and downloads the selected files into an uncompressed zip file.

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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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)

2. Subtomograms of T. kivui ribosome particles at bin1

Category:

subtomograms

Image format:

MRC

No. of images or tilt series:

25141

Image size:

(180, 180)

Pixel type:

SIGNED BYTE

Pixel spacing:

(3.52, 3.52)

Details:

Particle coordinates and final orientations are given in file ribo_tm_bin1_motl_12.star in STOPGAP format.

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. Denoised tomograms of T. kivui FIB-milled cells at bin4

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(928, 928)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(14.08, 14.08)

Details:

Tomograms were denoised with CRYO-CARE using reconstructions from odd and even frames.

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. Tilt series of T. kivui FIB-milled cells - session 2020-10-22

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(3712, 3712)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(3.52, 3.52)

Details:

Tilt series as MRC stacks containing motion-corrected and averaged frames for each tilt. Associated .mdoc files contain the metadata associated with data collection. Corresponding imod/ directory contains IMOD metadata for reconstruction.

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. Tilt series of T. kivui FIB-milled cells - session 2021-02-12

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(3712, 3712)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(3.52, 3.52)

Details:

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 raw frames of T. kivui FIB-milled cells tilt series - session 2020-10-22

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

1030

Image size:

(3838, 3710)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(3.52, 3.52)

Details:

File names follow the pattern ___.tif
Gain reference (DM4): CountRef_000_-10.0_Oct22_10.57.24.dm4
Gain reference (MRC): CountRef_000_-10.0_Oct22_10.57.24.mrc
Defects list: defects_000_-10.0_Oct22_10.57.24.txt

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. Unaligned raw frames of T. kivui FIB-milled cells tilt series - session 2021-02-12

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

1057

Image size:

(3838, 3710)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(3.52, 3.52)

Details:

File names follow the pattern ___.tif
Gain reference (DM4): CountRef_2021-01-12_10.54.03_tomo_01_000_-10.0.dm4
Gain reference (MRC): CountRef_2021-01-12_10.54.03_tomo_01_000_-10.0.mrc
Defects list: defects_tomo_001_026_36.0_Jan11_12.51.02.txt

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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