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

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

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From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-05-30

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Date: 2007-05-30

Subject: Re: How to determine ligand binding from diffraction pattern?
From: "Soisson, Stephen Michael" stephen_soisson {- at -} MERCK {- dot -} COM
Date: 2007-05-30

>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

In my opinion, this is not easy to reduce to a single number since there
are too many variables. True resolution and quality of the data, the
actual non-isomorphism (and in particular conformational changes),
B-factor of the ligand, etc.

The coy answer would be "enough refinement to convince yourself that it
is or isn't there", but in all seriousness, it does boil down to a
judgment call on when you have reached the point of diminishing returns.
I think the problem is particularly complex with the fragment screening
work you describe, since you may or may not know where the ligands are
actually binding. Tricky stuff indeed.

Steve

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CCP4bb navigation

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

Previous message:
Subject: Improving the GUI
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-05-30

Next message:
Subject: CCP4 GUI always show the job starts
From: Jhon Thomas jhon1 {- dot -} thomas {- at -} GMAIL {- dot -} COM
Date: 2007-05-30