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.


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Jason
Structural Biology Department
University of Pittsburgh
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