Dear Tom in addition to the very valuable input you have received already, I would like to point out that based on the fact that the <I/sigma_I> of your data is above 3 in the highest resolution shell, you will likely be able to push the resolution limits of your analysis to go beyond 1.4 angs resolution. I would definitely enoucrage you to do so even if Rmeas values end up being higher than what common practice and rules of thumb may prescribe. Recent work by Karplus and Diederichs (Science 336, 1030 (2012)) and an accompanying editorial by Phil Evans (Science 336, 986 (2012)) will provide the necessary food for thought to proceed.
Very best wishes Savvas ---- Savvas Savvides Unit for Structural Biology, L-ProBE Ghent University K.L. Ledeganckstraat 35, 9000 Ghent, Belgium Tel/SMS/texting +32 (0)472 928 519 Skype: savvas.savvides_skype http://www.LProBE.ugent.be/xray.html On 27 Mar 2013, at 17:22, Tom Van den Bergh <[email protected]> wrote: > Dear members of ccp4bb, > > I need some help with the refinement of my structure of a variant of mRFP > (monomer red fluorescent protein, sequence in attachment). I have done > molecular replacement with phaser with model 2VAD of protein database. Then i > have done some model building phenix.autobuild. (2 pdb's (overall...), freeR > flags and log file attached) When i refine with phenix.refine my structure i > get a R-value of 0,42 which is still way too high. (redfluorescent > protein.pdb, .mtz and logfile attached) When i look at the structure in coot > i find many unmodelled blobs and many outliers in density analysis and > rotamer analysis. The problem is that there are so many problems with my > structure, that i dont know where to begin. Could you try some refinement for > me, because this is first structure that i need to solve as a student and i > dont have too many experience with it. > > Greetings, > > Tom > > <overall_best.pdb><exptl_fobs_phases_freeR_flags.mtz><overall_best_placed.pdb><redfluorescentprotein_refine_10.pdb><redfluorescentprotein_refine_10.mtz><mRFPsequentiezondertag.fasta><redfluorescentprotein_refine_10.log><AutoBuild_run_6_1.log>
