What is the solution to this? Hi Meisam, you have it, it is just three molecules in the asu. Look at the overall crystal lattice packing and see if you have contacts supporting each molecule. Generate a large representation of your symmetry mates, I suspect you have a channel in your crystal lattice, explaining why your Matthews coefficient leads you in a wrong direction. If you are not convinced, calculate a selfrotation function with Molrep and look at the Chi=120 section and compare it to the Chi=90.
At least judging from your R-factors, if I understand you correctly you have not done much of a refinement yet. Have you performed a real space refinement and adjusted side chains etc. ? Jürgen ...................... Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu On Nov 21, 2013, at 12:35 PM, Meisam <meisam.nosr...@gmail.com<mailto:meisam.nosr...@gmail.com>> wrote: Dear CCP4ers I have a data set that diffracts 1.96 Å. It scales in P21 Space group with 7% linear Rfactor. The Mattew coefficient gives 10% probability for 3 molecules in the asymmetric unit, 53% for 4 molecules, and 36% for 5 molecules. Molecular replacement just finds 3 molecules in the asymmetric unit. Running Phaser also gives a partial solution with 3 molecules. When I refine just the back bone of the protein for the 3 molecules the Rfree/Rwork does not go better than 34% / 31%, and when I run the molecular replacement on the refined structure again, and I fix it as a model to search for another molecule, it still does not find it. I have attached a photo to show the density for the fourth molecule in the asymmetric unit. What is the solution to this? Thanks in advance for your help Meisam <An Extra Molecule.png>
