[3dem] Public 2D crystal dataset of MloK1 available at the EBI

Henning Stahlberg henning.stahlberg at unibas.ch
Tue Jan 28 07:48:02 PST 2014


Hi,

In a recent work, Julia Kowal and others from our lab studied the MloK1 bacterial potassium channel, which has putative voltage sensors and cAMP ligand binding sites, in the presence and absence of the ligand, by electron crystallography.

For the two configurations, we recorded a total of 78 respectively 67 images of 2D crystals tilted up to 45 degrees on photographic film and digitized them with a film scanner. Image processing in 2dx of the real-space images led to 3D maps of the protein in the two configurations at 7A resolution in plane, and 12A vertical resolution. We believe we processed this conservatively, leading to maps with little noise.  The maps are described in
http://www.nature.com/ncomms/2014/140128/ncomms4106/full/ncomms4106.html
The final volumes are deposited at the EMDB under EMD-2526 and EMD-2526, and the fitted atomic models are at the PDB under 4CHV and 4CHW.

We also have deposited the used 145 raw micrographs (TIFF format) with the corresponding 2dx processing file structure, including 2dx_image.cfg parameter files, merged APH files, phase origins, tilt angles, lattice line data, and final volumes, in short the entire 2dx image processing project, in one 12 GB ZIP file as a public dataset at the EBI under
http://www.ebi.ac.uk/~ardan/aspera/em-aspera-demo.html
accession code 10006.

If you download that ZIP file and unpack it, you should have the entire 2dx processing project on your computer. You should be able to inspect or re-run every 2d crystal processing step on those files with the 2dx software (which is based on the MRC software package). 2dx is available at 2dx.org<http://2dx.org>.
We invite you to look at those images and our processing, and are welcoming feedback on our image processing approaches.

All the best,

Henning.


Henning Stahlberg, PhD
Prof. for Structural Biology, C-CINA, Biozentrum, University Basel
Mattenstrasse 26 | D-BSSE | WRO-1058 | CH-4058 Basel | Switzerland
http://c-cina.org<http://c-cina.org/> | Tel. +41-61-387 32 62 | mailto:Henning.Stahlberg at unibas.ch


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