Well, trying to solve a MR structure with low homology (20%) and several molecules is always a challenge... Use any information you have. How many molecules are possible/probable given the mol.wt and unit cell? (Matthews coeff gives suggestions..) But remember solvent content can vary from 30% to 70% and more.
Is the structure likely to form dimers? trimers? etc. Biochemistry can help, and the self rotation can also give clues, although it can be a pain to interpret.. And if so is there a dimer model or trimer or whatever? May be better to search for fewer copies of the oligmer.. But if you get some sort of reasonable solution, then start refinement and rebuilding - if you can improve a single copy then you can use that as a new and better search model.. I would expect bigger increases in the LLG and TGscore if the 5th and 6th molecule were correct but maybe not.. You know you have solved it when the rebuilding bites.. \Good luck Eleanor On Wed, 13 Nov 2019 at 17:42, Tanner, John J. <tanne...@missouri.edu> wrote: > Dear Rob, > > Based on our experience with difficult MR cases, I recommend performing > refinement on the coordinates from MR (I prefer PHENIX simulated annealing > for this step). Then send the refined map - WITHOUT the model - to > automated building with density modification. The auto-built model may give > you an indication of how many chains are in the asymmetric unit. You could > do this procedure for each of the MR solutions (N=4,5,6) and compare the > results. Also, if you enable automatic detection of NCS during DM, you may > find that 6 NCS operators are found even when N=4 or 5; this would give you > confidence that N=6 is possible. > > Also look at the cross rotation function to see how many strong peaks are > present. I’m sure the peaks are listed in Phaser, but it is easier for me > to find them in the MOLREP output. MOLREP also provides a matrix that > tells you which cross RF peaks are related by symmetry and which are > unique, which is helpful. > > And David Schuller mentioned inspecting the self-RF, which is a good idea. > > Finally, do you know anything about the oligomeric state of the protein? > If it is a pentamer, N=6 seems unlikely. If it is a dimer, N=5 in P212121 > seems unlikely. > > Jack > > John J. Tanner > Professor of Biochemistry and Chemistry > Associate Chair of Biochemistry > Department of Biochemistry > University of Missouri > 117 Schweitzer Hall > 503 S College Avenue > Columbia, MO 65211 > Phone: 573-884-1280 > Email: tanne...@missouri.edu > http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html > Lab: Schlundt Annex rooms 3,6,9, 203B, 203C > Office: Schlundt Annex 203A > > On Nov 13, 2019, at 8:33 AM, Robert S Phillips <p...@uga.edu> wrote: > > I have been working on a protein structure which has been hard to solve by > molecular replacement. > > Unit cell: (60.6, 172.34, 196.42, 90, 90, 90) > Space group: P 21 21 21 > > The problem is that the homologues have only ~20% identity, and there are > multiple chains in the asymmetric unit. The question is how many. It > could be 4, 5, or 6 chains. > > N solvent P > 4 0.602 3.09 0.225 > 5 0.502 2.47 0.388 > 6 0.403 2.06 0.229 > > I have run PHASER with 4, 5 and 6 chains. I allowed it to search all > possible space groups, and P212121 was the best solution. These are the > results. > > N LLG TFZ > 4 104.9 7.5 > 5 137.5 7.7 > 6 166.2 8.3 > > Am I correct to conclude that there are 6 chains in the asymmetric unit? > > Rob > > Robert S. Phillips > Professor of Chemistry and of Biochemistry and Molecular Biology > University of Georgia > Athens, GA 30602 > Phone: (706) 542-1996 > Fax: (706) 542-9454 > E-mail: rsphill...@chem.uga.edu > Web: http://tryptophan.net > <https://pod51004.outlook.com/owa/redir.aspx?C=ccbf42ffea5f48b1bf8e9bb950454bab&URL=http%3a%2f%2ftryptophan.net> > > ------------------------------ > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
