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   Wow, you're lucky.  The problem usually is to not have density
for a peptide when one desperately wants density. ;-)

   You should treat this peptide just like you would any other.
Build what you can see, and verify that the peptide obeys standard
geometry, phi/psi plots, etc.  It should have plausible interactions
with the other contents of the crystal.

   The map you calculated just prior to building your first model
of this peptide will be the bias-free map you would use in publication
to demonstrate the existence of this peptide.  You want that map to
be the best possible.  Delay building the peptide until as many other
problems can be fixed to ensure this map is a clear as possible.

   I think you should also get a sample to your friendly neighborhood
mass spec expert and see what they can do.  If you can purify it,
traditional protein sequencing would be good.  Once you tie down
the sequence a search of your organism's genome would be very
informative.

Dale Tronrud

Fabien Bergeret wrote:
> Hello
> 
> We’re resolving a structure of a soluble protein and in the electronic
> density map (maximum resolution at 2.2Å), we observe a supplementary
> density that does not belong to the protein. This density is present in
> two different crystalline forms obtained in different crystallization
> conditions.
> This density could be represented by an oligopeptide ~10 residues long
> for which there is no ambiguity about its polarity. Furthermore, side
> chains are quite easily visible and a sequence can therefore be assigned.
> The deduced sequence doesn’t belong to the sequence of the protein of
> interest, meaning that the oligopeptide has been co-purified and
> co-crystallized.
> 
> Has somebody met a similar situation? Could you please give us some
> advices in terms of refinement, validation, etc.?
> 
> Thanks in advance
> 
> Best regards
> 
> 
> Fabien
> PhD student
> [log in to unmask] <mailto:[log in to unmask]>