[phenixbb] How to locate and refine a ligand using anomalous scattering
phenix.upitt at gmail.com
Tue Feb 8 10:14:42 PST 2011
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
- 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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