EMPIAR-10389 - High resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica [multiple data sets in MRC and TIFF formats]

EMPIAR-10389

High resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica [multiple data sets in MRC and TIFF formats]

Publication:

High-resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica

Righetto RD, Anton L, Adaixo R, Jakob RP, Zivanov J, Mahi MA, Ringler P, Schwede T, Maier T, Stahlberg H

Nature communications 11 (2020)

PMID: 33037208

DOI: 10.1038/s41467-020-18870-2

Related EMDB entry:

EMD-10835

Deposited:

2020-01-30

Released:

2020-06-12

Last modified:

2021-02-12

Imageset size:

839.88 GB

Imageset DOI:

10.6019/EMPIAR-10389

Experimental metadata:

Download xml json

Contains:

micrographs - single frame
micrographs - multiframe

Image Sets

1. Aligned averages of Y. enterocolitica urease

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

4313

Image size:

(3838, 3710)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(0.639, 0.639)

Details:

Y. enterocolitica Urease dataset
********************************

Acceleration voltage = 300 kV
Cs = 2.7 mm
Physical pixel size = 0.639 A/px
Total exposure = 42 e- / A^2 distributed over 40 frames for 8 s
Detector = Gatan K2 with Quantum-LS energy filter (20 slit eV width)

Data structure:

alignaver/ : This directory contains dose-weighted aligned movie averages from MotionCor2, the coordinates of the Gautomatch picked particles (STAR and BOX formats), and the meta-data for the Bayesian polishing (STAR format).

gainref/ : This directory contains the gain references in DM4 and MRC formats, pixel defect lists in TXT format.

raw/ : raw movies in TIFF format

micrographs_multi+single_joined.star : this file contains all the micrographs used for processing with their respective _rlnBeamTiltClass label.

run_ct14_data.star : this file contains the metadata for the particles used in the final reconstruction.

NOTE: The directories contain all data from the multi- and single-shot movies together, as specified by the file name.

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.

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)

2. Raw multi-frame micrographs of Y. enterocolitica urease

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

4314

Image size:

(3838, 3710)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(0.639, 0.639)

Details:

Dose rate is 1.05 e-/A^2.

Y. enterocolitica Urease dataset
********************************

Acceleration voltage = 300 kV
Cs = 2.7 mm
Physical pixel size = 0.639 A/px
Total exposure = 42 e- / A^2 distributed over 40 frames for 8 s
Detector = Gatan K2 with Quantum-LS energy filter (20 slit eV width)

Data structure:

alignaver/ : This directory contains dose-weighted aligned movie averages from MotionCor2, the coordinates of the Gautomatch picked particles (STAR and BOX formats), and the meta-data for the Bayesian polishing (STAR format).

gainref/ : This directory contains the gain references in DM4 and MRC formats, pixel defect lists in TXT format.

raw/ : raw movies in TIFF format

micrographs_multi+single_joined.star : this file contains all the micrographs used for processing with their respective _rlnBeamTiltClass label.

run_ct14_data.star : this file contains the metadata for the particles used in the final reconstruction.

NOTE: The directories contain all data from the multi- and single-shot movies together, as specified by the file name.

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

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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