Dear Rohit, I am totally agree with Mark, that just R free and R work does not decide the structure solved, you have to see other parameters as Mark already suggested. What is and redundancy and also what is the mosaicity? please look at these parameters too.
Best Prem On Wed, Dec 14, 2016 at 10:07 PM, Ashok Nayak <ashokgocrac...@gmail.com> wrote: > Dear Rohit, > > Look at what percentage of the reflections are in the Rfree set, if its > less say 5 %; and you have a good redundancy you can use 10 %. You might > like to use the other Rfree set[1 if you have already used the 0 set] or > consider using the whole set of reflections as a free set if need be if you > suspect a bias in your Rfree set. > > As suggested earlier I would also look at how the Fobs and Fcalc correlate > as a function of resolution from the sigma A plot or CC* values. > > Sometimes overestimating the resolution would add up more noise and it > would give you bad R values. > > and If the molecule is elongated you might have diffraction anisotropy and > in that case The R values don't come down. > > I would also like to use Refmac along with Phenix; that helped in my case. > > So you would like to take them one by one and figure out carefully. > > Best Wishes > > Ashok Nayak > Post-Doctoral Fellow, > Department of Physiology and Biophysics > VCU Medical Centre,1101 E Marshall ST, > Richmond,VA > USA > > > > On Wed, Dec 14, 2016 at 11:12 AM, Morais, Marc C. <mcmor...@utmb.edu> > wrote: > >> 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> >> 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 >>> http://wwwuser.cnb.csic.es/~mjvanraaij >>> >>> >>> >>> >>> >>> >>> >>> > On 14 Dec 2016, at 16:02, rohit kumar <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 >>> >> >> > > > -- > >
