Re: [ccp4bb] unknown density

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: unknown density
From: "Mark J {- dot -} van Raaij" mark {- dot -} vanraaij {- at -} USC {- dot -} ES
Date: 2010-02-03

Next message:
Subject: Re: Vapor diffusion calculator
From: Jacob Keller j-keller2 {- at -} MD {- dot -} NORTHWESTERN {- dot -} EDU
Date: 2010-02-03

Subject: Re: unknown density
From: Vellieux Frederic Frederic {- dot -} Vellieux {- at -} IBS {- dot -} FR
Date: 2010-02-03

Hi Katja,

What I personally do in such a situation is to start to fill the density
by water oxygen atoms, refine a bit (the position plus the isotropic
temperature factors) and then compute a new map. Usually it has cleared
up somewhat, thus allowing you to find out what it really is. This is
what happened to me recently with a whole stretch of polypeptide that
was in a different position in the MR search model and in the structure.
After introducing water molecules, refinement and a new map, bingo: the
whole stretch could be modelled.

And PEG tails can be disordered too.

Fred.

Katja Schleider wrote:
> Dear all,
>
> I found some fairly substantial density in the active site of my
> protein structure. But I don´t know what it should be. My
> crystallisation condition consists of lithium sulfate,
> citrate-phosphate and peg1000. The whole lot doesn't make a dashed bit
> of sense! Any suggestions to fill this density with something?
> Picture is attached.
>
> Thanks a lot,
>
> Katja
>
>

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: unknown density
From: "Mark J {- dot -} van Raaij" mark {- dot -} vanraaij {- at -} USC {- dot -} ES
Date: 2010-02-03

Next message:
Subject: Re: Vapor diffusion calculator
From: Jacob Keller j-keller2 {- at -} MD {- dot -} NORTHWESTERN {- dot -} EDU
Date: 2010-02-03