[phenixbb] sequence independent model building possible?

[Christian Roth]

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.

Christian
On 5 Feb 2016 06:02, "Kaushik Hatti" <hskaushik at gmail.com> wrote:

> 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 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
>
> --
> Stupidity is everyone’s birthright.  However, only the learned exercise it!
> --Kaushik (28Oct2014)
>
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