To check if you crystallized a contaminant, use https://strube.cbrc.kaust.edu.sa/contaminer/ HTH, Kay
Hello,
Is abinitio model building possible for a map with poly alanine model at 1.9A resolution?
We thought we had crystallised our protein of interest X, collected data at 1.9 A and all attempts to solve protein X (which has many homologs) through MR failed. All attempts to re-crystallise the same
On 02/05/2016 01:01 AM, Kaushik Hatti wrote: protein also failed.
Now, we think the initial protein which got crystallised could be a
contaminant (we don't have any crystals left from this batch to check for the sequence of the crystallised protein). Through various methods (and a bit of luck) we have arrived at a decent map with LLG : 3600 and TFZ: 22 and R/Rfree : 37/41 (for a poly alanine model).
I believe these scores indicate right fold. As I still don't know
the sequence information, is it possible to build sidechains directly from the map (I could only identify a couple of residues and the model largely remains PolyAla)? Autobuild with Rebuild-in-place didn't help in identifying any more residues.
I have also searched PDB database for similar structures. But, none
of those are either from our expression system (E. coli) or organism of our protein of interest. Neither did I find any similar sequences from E. coli or our organism of interest.
Any leads/suggestions would be helpful. Thanks, Kaushik, MRN Murthy lab, MBU, IISc, India
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