Oxalate. Sometimes forms when PEGs get old and begin to oxidize. That's some
of the stuff that is responsible for PEG's becoming progressively more
acidic as they age.
No idea if you have PEG in solution or not.
Alternative - CH3-C(=O)-COOH
Disordered dimethyl formamide
Dimethyl acetamide (CH3)2-N-C(=O)-CH3
And so forth.
Artem
-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Wu,
Mousheng
Sent: Thursday, July 26, 2007 6:35 PM
To: [log in to unmask]
Subject: Re: [ccp4bb] unknown density in structure
There are four molecules in the asymmetric unit. And this density is
present in every molecules.
-----Original Message-----
From: ANA MARIA MISIC [mailto:[log in to unmask]]
Sent: Thursday, July 26, 2007 5:24 PM
To: Wu, Mousheng
Subject: Re: [ccp4bb] unknown density in structure
Hi Mousheng - Did you check to see if that falls on a special position?
That can lead to a buildup of electron density, and the symmetrical
shape is suspect.
good luck
Ana M. Misic
Research Assistant
Department of Biomolecular Chemistry
Department of Bacteriology
University of Wisconsin - Madison
420 Henry Mall, Rm 230
Madison, WI 53706
Lab Phone: (608)265-9282
Fax: (608)262-9865
----- Original Message -----
From: "Wu, Mousheng" <[log in to unmask]>
Date: Thursday, July 26, 2007 4:21 pm
Subject: [ccp4bb] unknown density in structure
To: [log in to unmask]
> Hi, everyone,
>
>
>
> I am recently solving a structure at 1.8A. After I fitted all residues
> into the model, I found that there was an extra density in a pocket
> consisted of E, N, R and other hydrophobic residues. The density is
> strong and connected like a butterfly. I checked the crystallization
> condition. I can not figure out what it is. It seems that it is not
from
> the crystallization components.
>
>
>
> Does anyone know how to figure out what the density is? Is there any
> program or database I can use to predict the potential ligand?
>
> Thanks.
>
>
>
> Mousheng
>
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