Dear all, Greetings from Munich. I hope everything is well with you. I am writing to take input on a problem related to the structure solution of a protein-ligand complex.
I have crystallized a protein (7.6kDa) with a ligand (5.2kDa). The crystal diffracted to *2.71 Angstron*, and the data were processed using XDS. During the XDS processing, Pointless suggested data be either P6222 (180 space group) or P6422 (181 space group) with a 98% probability. The data were processed as *P6422*. Afterward, I ran Phaser MR with protein's PDB as a search ensemble, and I found a good solution (with a good TFZ score) for protein alone, where I could see some weak density for my ligand. In the next step, I ran Phaser MR with a *modeled PDB* of the Ligand as search ensemble + *using the partial solution from the previous Phaser MR run of Protein*. This Phaser MR run gave me a good fit of ligand onto protein surface with nice density for both molecules. Next, I went ahead with the refinement of this complex. The R-free, in the beginning, was 0.55. In the first round of refinement, it went down to *0.53,* but in the subsequent rounds, it even* increased*. I am stuck at this point and unsure how to proceed. I tried different strategies to refine it, but nothing worked. Could the space group have been wrong? How can I make sure that? I can provide a more detailed explanation to help you better understand the problem. I appreciate your suggestions and input on this matter. Kind regards, Deepak, Ph.D. student, LMU Munich, Germany. ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
