Re: [ccp4bb] How to determine ligand binding from diffraction pat tern?

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

Previous message:
Subject: Re: scala and cell dimensions
From: Jan Abendroth janabend {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2007-05-29

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From: Youssef BEN AMMAR youssef {- at -} RI {- dot -} NCVC {- dot -} GO {- dot -} JP
Date: 2007-05-30

Subject: Re: How to determine ligand binding from diffraction pat tern?
From: "Schubert, Carsten [PRDUS]" CSCHUBER {- at -} PRDUS {- dot -} JNJ {- dot -} COM
Date: 2007-05-29

Aha Dr. Palm ....

Tough to generalize this, but if the ligand is weak or the site only
partially occupied you need to refine almost to completion. Since you seem
to be doing something akin to fragment screening I can only pass on my
experience. I had plenty of cases where the Rfree was ~35 after a rigid body
refinement and the ligand density was practically indistinguishable from
bound water. Refinement to an Rfree of ~25 with waterpicking/pruning
resulted in clear enough density to place the ligand. This is probably
overkill for very tight binders but necessary for weak binders.
phenix works pretty well for this since one can do rigid body refinement,
individual positional refinement and B-refinement all in one shot.

Ciao

Carsten

> -----Original Message-----
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK]On Behalf Of
> Palm
> Sent: Tuesday, May 29, 2007 4:25 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] How to determine ligand binding from diffraction
> pattern?
>
>
> I would like to expand on the question and answer below and compare
> your experiences: Looking for ligands in many different soaks
> / cocrystals
> of your protein of interest, you still should do molecular
> replacement
> and a bit of refinement. I agree with Steve, but how much refinement
> is necessary and enough?
>
> We have a specific case with a 24 kDa protein crystallizing in P6522
> with resolution of 2.5 - 3 A, which should be comparable to most
> cases. The ligands have 10 - 20 non-hydrogen atoms (most of the time
> we don't know, we are actually screening for them). How far should
> we refine to see if we have only water molecules or a ligand bound
> - to an Rfree of 0.45 or 0.40 or 0.35?
> greetings
> Gottfried
>
>
> Dear all,
>
> Is there a simple way to determine whether ligand is bound or not
> by comparing the diffraction patterns between ligand-free (structure
> known) and ligand-soaked protein crystals? I would like to solve
> the ligand bound protein structure, but before I do so, I have to
> find out if the ligand is actually bound. Thank you very much!
>
> Best,
>
> Joe
>
> Having done this a few hundred times, I would strongly suggest that
> you just collect the data and solve the structure. Since you already
> have the apo structure solved, then it really isn't that much work
> to do an MR solution on the complex. Be aware that quite frequently
> there is enough non-isomorphism to necessitate partial refinement
> of the "complex" structure before recognizable density will appear
> for the ligand. The definitive answer can only be obtained with
> a full data set, so go for it.
>
> Good luck-
>
> Steve
>
>
>
>
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CCP4bb navigation

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

Previous message:
Subject: Re: scala and cell dimensions
From: Jan Abendroth janabend {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2007-05-29

Next message:
Subject: fit-protein in coot
From: Youssef BEN AMMAR youssef {- at -} RI {- dot -} NCVC {- dot -} GO {- dot -} JP
Date: 2007-05-30