I managed to solve a structure by MR at 2.4 A with a 27% identity model. Like you, I had to use a dimer search model to make any headway. To get usable maps and an initial model, I used Chainsaw to truncate the search model, Phaser (MR), Parrot (DM) with NCS averaging, then auto building with Buccaneer. I had the advantage of 8 chains in the ASU, which greatly improved the NCS averaging. NCS helps as the square root of the chains averaged.
Before going down this road, all potential MR solutions were carefully checked by examining crystal lattice packing to ensure the MR solution was reasonable and space group was likely correct, and that I had the correct number of chains per ASU. My initial MR attempts, based on Matthew's number estimates, were 2 chains short, which was obvious from crystal packing. Cheers, and good luck! Roger Rowlett Dorothy & Gordon Kline Professor, Emeritus Colgate University On Thu, Jun 18, 2020, 9:01 AM Robert S Phillips <[email protected]> wrote: > I've been pulling out my hair with this for a few months now. I have data > sets to 2.6 A for a new enzyme in the aminotransferase superfamily. > Unfortunately, the closest structure is only 25% identity. MR with PHASER > using the monomer was a complete failure. Since the minimum structure of > enzymes in the family is a dimer (the active site is formed at the > monomer-monomer interface), I used dimers for MR with PHASER. Most of the > results were marginal, but one looks good. However, it will not refine. > Everything I have done with this solution has failed, simulated annealing, > morphing, etc., it will not refine; AUTOBUILD and BUCCANEER with it do not > give any useable models, since they have poor statistics and low > completeness. The output from PHASER is below. > > ** SINGLE solution > > ** Solution written to PDB file: DGL_phaser.1.pdb > ** Solution written to MTZ file: DGL_phaser.1.mtz > Solution annotation (history): > SOLU SET RFZ=18.9 TFZ=23.0 PAK=0 LLG=193 TFZ==8.3 LLG=994 TFZ==20.1 > PAK=0 LLG=994 TFZ==20.1 > SOLU SPAC P 2 2 21 > SOLU 6DIM ENSE ense_1 EULER 360.0 0.0 0.0 FRAC -0.00 -0.00 -0.00 > BFAC -0.12 MULT 2 #TFZ==20.1 > SOLU ENSEMBLE ense_1 VRMS DELTA -3.5403 #RMSD 2.08 #VRMS 0.89 > > With LLG = 994 and TFZ = 20.1, isn't this a real solution? > > 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: [email protected] > 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/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## 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/
