Hi Rohit, Along with many excellent suggestions you already got...I want to add the possibility of the presence of twining (even a small but significant percent) and/or the presence of t-NCS in the data.
Good luck! Sudipta. On Wed, Dec 14, 2016 at 12:19 PM, Prem Prakash <prem...@gmail.com> wrote: > 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 >>>> >>> >>> >> >> >> -- >> >> >
