Re: [ccp4bb] suggestions on refinement of a protein-ligand complex

2022-09-13 Thread Eleanor Dodson
We probably need more detail to help you. Have you looked carefully at the data processing? Is the Rmerge or Rpim reasonable for all batches? Is there any suggestion of twinning? Does the wilson plot look linear? (These hexagonal SGs can be twinned) How many copies of your molecule do you expect

Re: [ccp4bb] suggestions on refinement of a protein-ligand complex

2022-09-13 Thread Kay Diederichs
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 like

[ccp4bb] suggestions on refinement of a protein-ligand complex

2022-09-13 Thread Deepak Deepak
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 p