[phenixbb] sequence independent model building possible?
jon.agirre at york.ac.uk
Fri Feb 5 13:31:34 PST 2016
if you're suspecting you've crystallised something else, perhaps you could
try running your crystal parameters through the nearest-cell server (
http://app.strubi.ox.ac.uk/nearest-cell/nearest-cell.cgi), which will scan
the PDB for crystals that match the input one.
On 5 February 2016 at 20:06, Christian Roth <christianroth034 at gmail.com>
> 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.
> On 5 Feb 2016 06:02, "Kaushik Hatti" <hskaushik at gmail.com> wrote:
>> 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
>> 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.
>> MRN Murthy lab,
>> IISc, India
>> Stupidity is everyone’s birthright. However, only the learned exercise
>> --Kaushik (28Oct2014)
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Dr Jon Agirre
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, England
+44 (0) 1904 32 8253
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