EMPIAR-10420 - Single-Particle Cryo-EM of Arabinosyltransferase EmbB from Mycobacterium smegmatis, Collected using both Falcon III and K2 Detectors [multiple data sets in MRCS, TIFF and MRC formats]

EMPIAR-10420

Single-Particle Cryo-EM of Arabinosyltransferase EmbB from Mycobacterium smegmatis, Collected using both Falcon III and K2 Detectors [multiple data sets in MRCS, TIFF and MRC formats]

Publication:

Cryo-EM structure of arabinosyltransferase EmbB from Mycobacterium smegmatis

Tan YZ, Rodrigues J, Keener JE, Zheng RB, Brunton R, Kloss B, Giacometti SI, Rosário AL, Zhang L, Niederweis M, Clarke OB, Lowary TL, Marty MT, Archer M, Potter CS, Carragher B, Mancia F, Tan YZ, Rodrigues J, Keener JE, Zheng RB, Brunton R, Kloss B, Giacometti SI, Rosário AL, Zhang L, Niederweis M, Clarke OB, Lowary TL, Marty MT, Archer M, Potter CS, Carragher B, Mancia F

Nature communications 11 (2020) 3396-3396

PMID: 32636380

DOI: 10.1038/s41467-020-17202-8

Related EMDB entry:

EMD-21983

Deposited:

2020-05-14

Released:

2020-07-30

Last modified:

2020-07-30

Imageset size:

4.51 TB

Imageset DOI:

10.6019/EMPIAR-10420

Experimental metadata:

Download xml json

Contains:

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

Image Sets

1. Unaligned and compressed multiframe movies from Falcon III Detector

Category:

micrographs - multiframe

Image format:

MRCS

No. of images or tilt series:

2159

Image size:

(4096, 4096)

Pixel type:

SIGNED 16 BIT INTEGER

Pixel spacing:

(0.665, 0.655)

Details:

Images were recorded in two sessions. This first session was on a Titan Krios electron microscope (FEI) equipped with a Falcon III direct detector operating at 0.665 Å per pixel in electron counting mode using the Leginon software package. Pixel size was calibrated after obtaining a preliminary map by docking with a crystal structure of a homolog of the soluble part of EmbB (PDB ID: 3PTY). Data collection was performed using a dose of ~78.02 e-/Å2 across 80 frames (1080 msec per frame) at a dose rate of ~0.40 e–/pix/sec, using a set defocus range of -0.5 μm to -2.5 μm. 100 micron objective aperture was used. The movies were recorded over three days using an image beam shift data collection strategy.

These files have been CTF corrected using the parameters in: data/02_Aligned_Micrographs/micrographs_ctf_18nov21d_FalconIII.star

Files:

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2. Unaligned and compressed multiframe movies from K2 Summit Detector

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

7943

Image size:

(3710, 3838)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(0.667089, 0.667089)

Details:

Images were recorded in two sessions. This second session was on a Titan Krios electron microscope (FEI) equipped with a K2 summit direct detector operating at 0.667 Å per pixel in counting mode using the Leginon software package. Pixel size was calibrated in-house using a proteasome test sample. Data collection was performed using a dose of ~77.53 e-/Å2 across 80 frames (100 msec per frame) at a dose rate of ~4.3 e–/pix/sec, using a set defocus range of -0.3 μm to -2.9 μm. 100 micron objective aperture was used. The movies were recorded over three days using an image beam shift data collection strategy.

These files have been CTF corrected using the parameters in: data/02_Aligned_Micrographs/micrographs_ctf_19may24c_K2.star

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. Aligned and dose-weighted micrographs from Falcon III Detector

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

1955

Image size:

(4096, 4096)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(0.665, 0.665)

Details:

For this first Falcon III dataset, movie frames were aligned using MotionCor2 with 5 by 5 patches and B-factor of 500 for global alignment and 100 for local alignment through the Relion package.

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. Aligned and dose-weighted micrographs from K2 Summit Detector

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

6025

Image size:

(3710, 3838)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(0.667089, 0.667089)

Details:

For the second K2 summit dataset, movie frames were aligned using MotionCor2 with 5 by 5 patches and B-factor of 500 for global alignment and 100 for local alignment through the Relion package.

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. Final Particle Stack with Refined Euler Angles and Shifts

Category:

picked particles - single frame - processed

Image format:

MRCS

No. of images or tilt series:

Image size:

(256, 256)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.0, 1.0)

Details:

Combined particle stack from both datasets.

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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