Dear All, I am very happy to inform you that I have finally solved the structure. Thanks to all for your kind suggestions.
With best regards, Shankar On Wed, Aug 3, 2016 at 8:35 PM, Sudipta Bhattacharyya < [email protected]> wrote: > Dear Shankar, > > The high TFZ and LLG you mentioned indeed indicate a possible solution. > However, how certain are you about the number of ensembles placed in the > ASU? Also this high Rfree value sometime indicates the presence of > t-NCS/twining, Did you check that (the presence of large off origin t-NCS > peak)? Although phaser should detect it and correct it accordingly but only > if you are searching for even number of ensembles in the ASU. > > Good luck, > Sudipta. > > On Wed, Aug 3, 2016 at 9:14 AM, Shankar Prasad Kanaujia < > [email protected]> wrote: > >> Dear All, >> >> As suggested, I tried several things. I am getting MR solutions with TFZ >> > 8.0 (e.g. 12, 16) and high LLG (e.g. 150, 160). However, Rw/Rf remains >> above 0.50 after first round of refinement. In some cases, after some >> manual model building, Rw falls up to 0.46, however, Rf remains above 0.50. >> >> Any suggestions for further model building. The data is of ~1.9 Angst >> processed in P1211. >> >> With best regards, >> Shankar >> >> On Mon, Aug 1, 2016 at 1:48 PM, <[email protected]> wrote: >> >>> Dear Schankar, >>> >>> >>> >>> you could also try automatic packages like Balbes or Morda. However, it >>> might not be a bad idea to try a more rational approach as well. With 27% >>> sequence identity, you template may or may not have the same fold. With 27% >>> sequence identity AND a similar biological function (e.g. similar reaction >>> catalysed, binding to a similar receptor etc.), your bets are much better. >>> (Except cases with large conformational changes like antibodies and >>> calmodulin). >>> >>> >>> >>> If molecular replacement fails, you should also look very carefully in >>> the space group assignment and in case of ambiguity try all possible space >>> groups for your MR searches. >>> >>> >>> >>> Best, >>> >>> Herman >>> >>> >>> >>> >>> >>> >>> >>> *Von:* CCP4 bulletin board [mailto:[email protected]] *Im Auftrag >>> von *Sivakumar N >>> *Gesendet:* Montag, 1. August 2016 08:30 >>> *An:* [email protected] >>> *Betreff:* Re: [ccp4bb] Molecular replacement with template having low >>> sequence identity >>> >>> >>> >>> Dear Shankar, >>> >>> How do you appreciate this approach of generating an Ensemble of >>> superposed homologous structures as a MR search probe? I found the FUGUE >>> server helpful in pulling out the distantly related structural homologues >>> for a given query sequence. Also, a manual or an automated method of >>> refining or sieving the superposed homologues to cut out the residues that >>> fall in the loop regions and possibly other residues at loci that introduce >>> any noisy-correspondences between the superposed structures can be useful, >>> in order to arrive at a better RMSD values between the equivalent Cα atoms >>> of this hybrid MR search probe. >>> >>> Regards >>> >>> Sivakumar,N. >>> >>> >>> >>> On Sat, Jul 30, 2016 at 6:20 PM, Shankar Prasad Kanaujia < >>> [email protected]> wrote: >>> >>> Dear All, >>> >>> Is it possible to solve the structure of a protein having template with >>> a sequence identity of 27%. If yes, what is the best possible method. >>> >>> Any program which can automatically give some clue. >>> >>> With best regards, >>> >>> Shankar >>> >>> >>> >> >> >> >> -- >> Shankar Prasad Kanaujia, Ph.D. >> Assistant Professor >> Department of Biosciences and Bioengineering >> Indian Institute of Technology Guwahati >> Guwahati - 781039 Assam, India >> Tele: 0361 258 2228 >> Fax: 0361 258 2249 >> Email: [email protected] >> Homepage: http://www.iitg.ernet.in/spkanaujia/ >> Google Scholar: https://scholar.google.com/citations?user=Zt4JSNYAAAAJ&; >> hl=en >> > > -- Shankar Prasad Kanaujia, Ph.D. Associate Professor Department of Biosciences and Bioengineering Indian Institute of Technology Guwahati Guwahati - 781039 Assam, India Tele: 0361 258 2228 Fax: 0361 258 2249 Email: [email protected] Homepage: http://www.iitg.ernet.in/spkanaujia/ Google Scholar: https://scholar.google.com/citations?user=Zt4JSNYAAAAJ&hl=en
