[phenixbb] How to locate and refine a ligand using anomalous scattering

Christian Roth christian.roth at bbz.uni-leipzig.de
Tue Feb 8 13:11:09 PST 2011

Hi Jason,

I am not an expert, but in my opinion it is enough to collect 1 dataset at the 
peak wavelength for bromide. Should be anomalous complete for sure. Process it 
without merging Friedel pairs. Solve the structure via molecular replacement 
with your known protein structure. 
Next step ist to create a map using the anomalous differences in your mtz with 
the phases from your mtz after refinement.
Now you should see a peak in the density for your Bromine, if ligand is there. 
Than you have the position of your ligand There should be hopfully density 
from you normal maps. Put your ligand in it. The bromine dictates the 
orientation. Put this with the generated library file(phenix.elbow) in phenix 
and refine it. 

I think this should work.

Good Luck and all the best. 


P.S. Despite the fact that you did cocrystallisation, the ligand might not be 
there, or even at a position which is not the right one. Unfortunately I had 
already such a case.

Am Dienstag 08 Februar 2011 19:14:42 schrieb Jason:
> Hello everyone,
> I have a few crystals to be x-rayed next week. Before that I hope to get a
> clear idea about what I am doing (I am new to anomalous scattering).
> Facts:
>    1. The crystal is a protein co-crystallized with a ligand
>    2. The protein structure is known.
>    3. The ligand has a heavy atom bromide (absorption K-egde=13.47Kev)
>    4. Data resolution is ~3 angstrom
> Goals:
>    1. Locate the bromide position
>    2. Locate and refine the ligand
> Questions:
>    1. Do I need to carry out MAD experiment at 3 wavelengths or there is
>    some other easier way since the protein structure is known (I am not
>    expecting big change of the protein structure     itself)?
>    2. Assuming I have the MAD data, what should I do next using phenix to
>    achieve the two goals listed above? Here are some thoughts:
>       - Using phenix.hyss to locate the anomalous scatterers
>       - Using phenix.autobuild to build the protein model (which data set
>  to use?)
>       - Using coot to add ligands to the protein structure (Is the relative
>       position between the protein and the ligand known based on
> phenix.hyss and
>       phenix.autobuild?)
>       - Using phenix.refine to refine the ligand+protein complex
> Thank you all for reading this.
> ======================
> Jason
> Structural Biology Department
> University of Pittsburgh
> ======================

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