In addition to what others have mentioned, you might want to consider the unpleasant possibility that part of your structure is simply built incorrectly. Sometimes rebuilding a short loop or even a few residues in that loop can do the trick. Look carefully for regions of your map with poor density and/or regions of your model with poor geometry, and see if there might be an alternate way to build that region. There is often a psychological barrier to attempting these rebuilds, because they are difficult (if they weren't we would have built correctly the first time). However, once begun, it is often less painful than expected. SA/composite omit maps can help. ________________________________ From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Eleanor Dodson [eleanor.dod...@york.ac.uk] Sent: Wednesday, December 14, 2016 9:49 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] R/Rfree values
es - look carefully at your data quality indicators - batch scales, Wilson plot - moments etc.. tHese can show up if there is a problem with ice rings or crystal decay or whatever. Then I always look at the REFMAC plot of <Fobs> v <Fcalc> If they overlap well - good - but problems with scaling will show up there. Eleanor On 14 December 2016 at 15:21, Mark J van Raaij <mjvanra...@cnb.csic.es<mailto:mjvanra...@cnb.csic.es>> wrote: Dear Rohit, I wouldn’t judge a structure just by the Rwork and Rfree values, but also by the validation and other statistics (bond lengths, angles, Ramachandran plot, map quality, fit to map, average B values). If these are all ok, you should be able to “get away with” an Rfree of 33%. In your email you state that you have already made a significant effort in different refinement strategies, so perhaps there is no improvement to be made there. The reason for the high-ish Rfree could be that the data is not so good, and reprocessing might help. Although the most likely outcome is that you can’t significantly improve it, but at least trying will put your mind more at ease. In the end, the only way to improve the structure, and R-factors, may be to grow a better crystal, cryo-protect better and/or collect better data - this particular crystal may just have some kind of disorder. Greetings, Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616<tel:%28%2B34%29%2091%20585%204616> http://wwwuser.cnb.csic.es/~mjvanraaij > On 14 Dec 2016, at 16:02, rohit kumar > <rohit...@gmail.com<mailto:rohit...@gmail.com>> wrote: > > Dear All, > > I am solving a data of 2.5 A (C121 space group). Right now the R/Rfree values > are 26/33, after many cycles of refinements (With or With out water) the > R/Rfree values still same. Zanuda suggests that the space group seems to be > correct and the model is looking fine in coot. > Some one suggest what is the main problem. > Should I again process my data? And what is the best way to fine right space > group (If problem with space group). > Please tell me if you need any information regarding may data. > > -- > WITH REGARDS > Rohit Kumar Singh > Lab. no. 430, > P.I. Dr. S. Gourinath, > School of Life Sciences, > Jawaharlal Nehru University > New Delhi -110067
