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

Jason phenix.upitt at gmail.com
Tue Feb 8 10:14:42 PST 2011

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).


   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


   1. Locate the bromide position
   2. Locate and refine the ligand


   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
      - 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
      - Using phenix.refine to refine the ligand+protein complex

Thank you all for reading this.

Structural Biology Department
University of Pittsburgh
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