Hello Marco, this sounds to me like there is space group confusion in the sense that if you use the output model from Phaser, it may say space group P22121 (with a<b<c) in the PDB header but in your downstream calculations you may be using a MTZ file specifying space group P21212 (with a<b<c) . This will not refine.
If this is indeed your problem, then the way to resolve this is a) in XDS.INP, specify UNIT_CELL_CONSTANTS= b c a 90 90 90 !(where a<b<c !), SPACE_GROUP_NUMBER=18, JOB=CORRECT . Run XDS. b) remove UNIT_CELL_CONSTANTS and SPACEGROUP_NUMBER lines from XDSCONV.INP, and run XDSCONV. Or use pointless/aimless c) run Phaser again with the resulting MTZ file (check that it has spacegroup 18 i.e. P21212 and cell parameters with c shortest). Check that the resulting PDB file has P21212 and b c a cell parameters in the header. d) run refinement Hope this helps, Kay On Tue, 20 Feb 2024 01:15:49 +0000, Marco Bravo <mbrav...@ucr.edu> wrote: >Hello Todd, I get the best solution for p22121 space group after MR with an >LLG score of 640 from phaser. and the Rfree is .4748. However after MR >refinement does not lower the Rfree and it appears to make the Rfree worse. >The XDS software indicates that my best solution is P21 21 2. Often Phaser MR >places the solution in P 21 21 2. The helicase is a superfamily 2 helicase and >is only monomeric. Its a 543aa long protein with a MW of 62Kda. It should have >two RecA like domains at the core but the protein I have crystallized has a >previously uncharacterized n-terminal domain responsible for tight single >stranded DNA binding. I have tried different space groups manually but that >resulted in clashing. I will be frank I do need to work on my crystallography >background as crystal lattices, space group, and self-rotaion functions are >limited. Thank you so far for your help , I will try further trimming down my >search model into separate domain and trying that in the meantime. > >######################################################################## > >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/
