Dear Shanti Pal Gangwar, You are trying to solve your crystal structure of what! whether its a peptide or protein or enzyme or nucleic acid? There are several reasons behind getting a high Rmerge, it not only depends on the data quality. What are all the efforts! that you have applied to solved your crystal structure. Provide some more information like,
-atleast some preliminary info of data collection methods -the program(s) you tried to process your data set -space group/unit cell length/completeness for the low and high resolution shells/ I\s. -whether your molecule is a monomer/dimer/......in asymmetric unit -have you access the data quality (very easy in Xtriage-PHENIX), whether it contains any twinning / translational pseudosymmetry. -some info about your molecular replacement programs(s) output like correlation coefficient, Rfactor | LLG, RF, TF, PAK | -the refinement program(s) you tried -hows your electron density map look like after the initial rounds of refinement you could easily include all the above information within a two or maximum three lines. If your question is very clear than definitely you will get more inputs from the experts, so that you will be guided in a right way to get your crystal structure ASAP! Regards, Dr. S. M. Jaimohan On Tuesday, 4 February 2014 8:18 PM, Bernhard Rupp <hofkristall...@gmail.com> wrote: …the slash at the end is obviously the secret sign for “google-translate into a randomly picked language” http://scripts.iucr.org/cgi-bin/citedin?dz5235 From:Rick Lewis [mailto:r.le...@ncl.ac.uk] Sent: Dienstag, 4. Februar 2014 15:24 To: b...@hofkristallamt.org Subject: Re: [ccp4bb] high Rwork / Rfree after MR a third of nothing is till nothing... see attached screendump ;-) On 04/02/14 14:19, Bernhard Rupp wrote: EDSTATS is part of CCP4 > >….which in fact I cite in 33% of all of its CrossRef references > >http://scripts.iucr.org/cgi-bin/citedin?dz5235/ > >Touché. > >From:CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Frank von >Delft >Sent: Dienstag, 4. Februar 2014 14:40 >To: CCP4BB@JISCMAIL.AC.UK >Subject: Re: [ccp4bb] high Rwork / Rfree after MR > >And really we should not be using real space CC or real space R anymore - not >since Tickle 2012 (http://scripts.iucr.org/cgi-bin/paper?S0907444911035918) > >EDSTATS is part of CCP4. > >phx > > > > > >On 04/02/2014 13:31, Bernhard Rupp wrote: >> interpretable electron density map is obtained to which most of your protein >> model can be fitted properly. The primary numeric indication for that are >> your R-factors. >> >>Minor comment: The measure for the fit of the *model (density) to the >>electron density* is actually a local real space correlation coefficient or a >>local real space R value, not the global reciprocal space R-values (not a >>*factor* in the mathematical sense, nor a factor for anything else). The >>overall linear residual between model structure factor amplitudes Fc and >>observed amplitudes Fo (aka R(F)-value) is a global reciprocal space measure, >>which can be affected by many other contributions causing the misfit between >>Fo and Fc data, in addition to bad model, as already noted below. >> >>Ø The high values you have suggest that either something is wrong with your >>space group, twinning, etc. as Eleanor suggested, or your space group and MR >>solution may be still correct but for a search model of poor similarity with >>your crystal structure. Even in the later case, at this resolution it is >>going to be very challenging to build and refine a structure to reasonable >>R-factors starting from a poor model. >> >>Hay >> >> >>======================================== >>Hay Dvir Ph. D. >>Head Technion Center for Structural Biology >>Technion Haifa 3200003, Israel >>Tel: +(972)-77-887-1901 >>Fax: +(972)-77-887-1935 >>E-mail hd...@technion.ac.il >>Website http://tcsb.technion.ac.il/Hay-Dvir >>======================================== >> >> >> >> >>On Feb 4, 2014, at 11:36 AM, Shanti Pal Gangwar wrote: >> >> >> >> >> >>Dear All >>I have solved one structure by MR. The data data quality was poor so the >>Rmerge was high. The resolution of the data is 3.3 Angstrom.The refinement >>statistics are also very poor Rw/Rf= 40/42 %. After many efforts we are not >>able to get reasonable Rw/Rf. >> >>My question is "can it be claimed that we have solved the structure?" >> >> >> >> >>Thanks in advance >> >> >> >> >> >>-- >>******************** >>regards >>Shanti Pal Gangwar >>School of Life Sciences >>Jawaharlal Nehru University >>New Delhi-110067 >>India >>Email:gangwar...@gmail.com >> >> >> >> >> > -- R. J. Lewis Professor of Structural Biology Institute for Cell and Molecular Biosciences Faculty of Medical Sciences Tel: +44 (0)191 222 5482 University of Newcastle Fax: +44 (0)191 222 7424 Newcastle upon Tyne, NE2 4HH, UK Email: r.le...@ncl.ac.uk URL: sbl.ncl.ac.uk
