Hi Marco, I was just about to write with a different suggestion when Kay’s reply came in. What Kay suggests sounds like the best thing to do first!
However, if that isn’t the issue, then I’m wondering if it could be a problem with incorrectly diagnosed translational non-crystallographic symmetry (tNCS). The ambiguity about which axes are pure 2-folds or 2-fold screws is the kind of thing that occurs when there is an NCS translation with a component of 1/2 along at least one of the axes. I couldn’t find anything about how many copies you have in the asymmetric unit of the crystal, but is it an even number? Do any programs (including Phaser) find large native Patterson peaks away from the origin? Are the intensity distributions and/or moments unusual? You could send me a copy of the log file from a Phaser run if you don’t know where to find this information. Good luck! Randy Read > On 20 Feb 2024, at 09:11, Kay Diederichs <kay.diederi...@uni-konstanz.de> > wrote: > > 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 http://www.jiscmail.ac.uk/CCP4BB, a >> mailing list hosted by http://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 http://www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by http://www.jiscmail.ac.uk/, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk ######################################################################## 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/
