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

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Subject: Re: How to determine ligand binding from diffraction pattern?
From: Isaac Westwood isaac {- dot -} westwood {- at -} PHARM {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2007-05-29

Subject: Re: How to determine ligand binding from diffraction pattern?
From: Palm palm {- at -} UNI-GREIFSWALD {- dot -} DE
Date: 2007-05-29

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