Fabien,
The extra density may be from a his-tag or cloning artifacts left over
at the beginning or end of your protein sequence. You may be seeing the
residues coming from a neighboring molecule. I have seen parts of a
C-terminal his-tag ordered in the electron density before.
Jon Schuermann
--
Jonathan P. Schuermann, Ph. D.
Beamline Scientist
NE-CAT, Building 436E
Advanced Photon Source (APS)
Argonne National Laboratory
9700 South Cass Avenue
Argonne, IL 60439
email: [log in to unmask]
Tel: (630) 252-0682
Fax: (630) 252-0687
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]>
--
Jonathan P. Schuermann, Ph. D.
Beamline Scientist
NE-CAT, Building 436E
Advanced Photon Source (APS)
Argonne National Laboratory
9700 South Cass Avenue
Argonne, IL 60439
email: [log in to unmask]
Tel: (630) 252-0682
Fax: (630) 252-0687
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