Dear Luca, few possibilities: 1) Consider that you may have only 3 monomers in the asymmetric unit and not 4 as suggested from Matthew’s coefficient. Which are the R and Rfree values if you refine this model with only 3 molecules? 2) When you look at the crystal packing on the correctly placed monomers (let’s call them A, B and C), is one of them (imagine C) forming a similar homodimer as AB with another monomer C according to the crystal symmetry? 3) Following up on Ethan’s suggestion, if you see extra-density that could correspond to part of the 4th monomer, you can try to use the 2Fo-Fc electron density map to locate the 4th molecule using MolRep and its option “Search in a map”. In this case, feed MolRep with the coordinates of the 3 correctly placed monomers as fixed model. It worked many times in my case.
Hope this helps. Marc — Marc GRAILLE, PhD DR1-CNRS Laboratoire de Biologie Structurale de la Cellule (BIOC; Ex-Laboratoire de Biochimie) UMR7654 du CNRS Head of the team: “Translation and degradation of eukaryotic mRNAs” ÉCOLE POLYTECHNIQUE 91128 PALAISEAU CEDEX FRANCE 📞: +33 (0)1 69 33 48 90 : [email protected] <mailto:[email protected]> / : @GrailleLab <https://twitter.com/GrailleLab> https://portail.polytechnique.edu/bioc/en/research/coupling-between-translation-and-mrna-degradation-eukaryotes — > Le 6 janv. 2021 à 08:38, Luca Mazzei <[email protected]> a écrit : > > Hi all, > > I am struggling with the MR of a homo-dimer using Phaser. Matt_coeff strongly > suggests the presence of 4 mol per asym unit (space group P6222). The results > after a search of 4 mol per asymmetric unit of my monomer are the following: > > ** SINGLE solution > > ** Solution written to SOL file: phaser_3f6v_A1_MOLREP.sol > > ** Solution written to PDB file: phaser_3f6v_A1_MOLREP.1.pdb > ** Solution written to MTZ file: phaser_3f6v_A1_MOLREP.1.mtz > Solution annotation (history): > SOLU SET RFZ=3.9 TFZ=8.5 PAK=3 LLG=65 TFZ==10.0 RFZ=2.6 TFZ=17.0 PAK=3 > LLG=326 TFZ==29.8 (& TFZ==22.5 & TFZ==19.7) > LLG+=(326 & 529 & 593) LLG=795 TFZ==5.4 PAK=5 LLG=795 TFZ==5.4 PAK=5 > LLG=795 TFZ==5.4 > SOLU SPAC P 62 2 2 > SOLU 6DIM ENSE autoMR EULER 125.3 60.8 300.2 FRAC 0.17 -0.13 0.08 > BFAC -9.34 #TFZ==10.0 > SOLU 6DIM ENSE autoMR EULER 305.4 60.8 300.2 FRAC 0.27 -0.16 0.08 > BFAC -5.29 #TFZ==29.8 > SOLU 6DIM ENSE autoMR EULER 294.7 119.1 120.3 FRAC 0.45 0.01 0.26 > BFAC 0.34 #TFZ==22.5 > SOLU 6DIM ENSE autoMR EULER 305.5 61.6 300.1 FRAC 0.11 -0.16 0.08 > BFAC 29.19 #TFZ==5.4 > SOLU ENSEMBLE autoMR VRMS DELTA -0.2463 #RMSD 0.93 #VRMS 0.79 > > It seems (also looking at the maps) that it correctly places three monomers > out of four. How can I use this information to improve the search of the > fourth monomer using the same template model? > > Thanks in advance for your help, > > Best regards > > Luca Mazzei > > Luca Mazzei - PhD > Laboratory of Bioinorganic Chemistry > Department of Pharmacy and Biotechnology (FaBiT) > Alma Mater Studiorum - University of Bologna > Viale Giuseppe Fanin, 40 - 40127, Bologna - Italy > Tel: +39 0512096235 > > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > <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/
