Dear Deepak, I guess that the spacegroup in the MTZ file that you use for refinement is wrong.
I think you should carefully check the output of PHASER, and in particular the PDB file that it wrote. The correct spacegroup is given there (and it may also be P4122 or P4222 or P4322, because likely you used the PHASER option that tests all possibilities), and you will have to create a MTZ file for refinement that has that particular spacegroup in its header. Hope this helps, & best wishes Kay On Tue, 13 Sep 2022 11:20:44 +0200, Deepak Deepak <deepmalik...@gmail.com> wrote: >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/ > ######################################################################## 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/
