Re: [ccp4bb] ligand refinemnet

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

Previous message:
Subject: Re: ligand refinemnet
From: Kontopidis George gkontopidis {- at -} VET {- dot -} UTH {- dot -} GR
Date: 2009-04-02

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Subject: Re: Lowest resolution you can do MR with
From: Bjørn_Panyella_Pedersen bjopp {- at -} BIOXRAY {- dot -} AU {- dot -} DK
Date: 2009-04-02

Subject: Re: ligand refinemnet
From: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2009-04-02

Hello Peter,

at 3A resolution occupancy refinement is supposed to fail, I'd say.
The large B-values can make up for reduced occupancy (as you already
pointed out to) but also large flexibility.

You might try ten refinement runs in parallel with fixed occupancies
varying from 10% to 100% and check whether you can detect signs of a local
minimum at a certain occupancy - e.g. real space CC, best fit of B-values,
etc. Yet much more you can probably not do.

If you cannot come to a satisfactory solution you may place a model ligand
and describe the situation in the PDB header. That's not ideal but
probably one of the best ways to go in my opinion.

Tim

--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

On Thu, 2 Apr 2009, peter hudson wrote:

> Hello all
>
> I have refined and built model a dataset of 3.0A resolution dataset. This
> model is assocaied with a ligand. After final refinement and model
> building i found a big blob of Fo-Fc density of around 4sigma level at
> the N-terminal of the fianl model. My protein doesnot carry any tag at
> the N-terminal. But, the template i have used for the molecular
> replacement carrying a tag at the N-termianl, which can occupy only 1/4th
> of this positive density after superpostion. My crystallisation
> conditions component cannot occupy such higher level of positive density.
> Since my protein binds to a ligand, i looked carefully to the positive
> density and it seems very similar to the ligand density but its obscure.
> Refinement after fitting the ligand leads to very high B-factor of the
> ligan, which vary for various atoms from 50-90 and simultaneously
> positive density goes off. I also tried to change the occupancy of the
> ligand but as i reduce the occupancy the B factor comes down at the
> noraml expected average B factor value but again Fo-Fc density appears in
> the map over ligand. If i leave to refine the occupancy to the programme
> automatically, this lead to the zero occupancy of the few atoms in the
> ligand and avearge B factor remains normal. suggestions would be
> appreciated.
>
> Thanks in advance
> Peter
>

CCP4bb navigation

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

Previous message:
Subject: Re: ligand refinemnet
From: Kontopidis George gkontopidis {- at -} VET {- dot -} UTH {- dot -} GR
Date: 2009-04-02

Next message:
Subject: Re: Lowest resolution you can do MR with
From: Bjørn_Panyella_Pedersen bjopp {- at -} BIOXRAY {- dot -} AU {- dot -} DK
Date: 2009-04-02