<p dir="ltr">Hi, besides the already excellent suggestions, you might want to try if density modification (NCs, solvent flattening, histogram matching) improves your map a bit further. If you can assign enough residues you improve your maps than even further step by step. On top your stretches are than definitely long enough for a blast search.</p>
<p dir="ltr">Christian</p>
<div class="gmail_quote">On 5 Feb 2016 06:02, "Kaushik Hatti" <<a href="mailto:hskaushik@gmail.com">hskaushik@gmail.com</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><p dir="ltr">Hello,</p>
<p dir="ltr">Is abinitio model building possible for a map with poly alanine model at 1.9A resolution?</p>
<p dir="ltr">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 protein also failed. </p>
<p dir="ltr">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).</p>
<p dir="ltr">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.</p>
<p dir="ltr">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.<br></p>
<p dir="ltr">Any leads/suggestions would be helpful.<br>
Thanks, <br>
Kaushik,<br>
MRN Murthy lab,<br>
MBU,<br>
IISc, India</p>
<p dir="ltr">-- <br>
<font color="#999999">Stupidity is everyone’s birthright. However, only the learned exercise it!</font><br>
<font color="#999999">--Kaushik (28Oct2014)</font></p>
</div>
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