Dear Gordon,
To me, the density does not look really symmetric, which would argue against a special position. However, in some other view, the density may turn out to be symmetric. The ligand seems to be in a crystal contact, which would argue against a co-purified ligand. I would look at the following options:
1) any buffer component, including the protein buffer
2) a random peptide, released by some proteolytic activity
3) a co-purified natural ligand or inhibitor added during cell-lysis/purification. The natural ligands of protein are usually known.
Best,
Herman
-----Ursprüngliche Nachricht-----
Von: CCP4 bulletin board [mailto:[log in to unmask]] Im Auftrag von Tim Gruene
Gesendet: Montag, 2. November 2015 09:16
An: [log in to unmask]
Betreff: Re: [ccp4bb] unknown electron density
Dear Gordon,
the position seems near or at a special position - one can see a symmetry related protein chain in the background.
When comparing with the crystallisation conditions, you would have to
- take the symmetry element into account
- combine it with possible disorder
- take 'artefact' into account that usually appear near special positions.
If you cannot immediately figure out, what you might be looking at, I would not worry too much.
Regards,
Tim
On Monday, November 02, 2015 01:16:37 AM Joyce, Gordon M. [E] wrote:
> Dear All,
>
> I am refining a structure and have come across strong electron density
> for an unknown ligand (see below). Would someone be able to identify
> this unknown ligand that somehow was co-purified with the protein. The
> electron density shape does not match anything included in the
> crystallization conditions.
>
> [cid:image001.jpg@01D114E2.3649B6A0]
>
>
> [cid:image002.jpg@01D114E2.3649B6A0]
>
>
> Thanks for your help in advance,
> Gordon
>
> M. Gordon Joyce, Ph.D.
> Virology Lab,
> Vaccine Research Center,
> NIAID/NIH
> 40 Convent Dr., Room 4613B
> Bethesda, MD 20892
> Phone: 301-594-8717
> Fax: 301-480-2658
> [log in to unmask]<mailto:[log in to unmask]>
>
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