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Dear Dilip Badjugar, Perhaps it may be good to take a look at the unmodelled blobs and see if there is any large densities left unexplained. Also how does the Rmerge vary with the resoln ? Is your data good upto 1.7A? Regards and wishes Krishnaswamy On 13 Oct 2013 04:33, "CCP4BB automatic digest system" < [log in to unmask]> wrote: > There are 3 messages totaling 137 lines in this issue. > > Topics of the day: > > 1. Celebrating Crystallography — A short animated film > 2. Rfree stuck (2) > > ---------------------------------------------------------------------- > > Date: Sat, 12 Oct 2013 11:37:18 +0000 > From: "Curry, Stephen" <[log in to unmask]> > Subject: Celebrating Crystallography — A short animated film > > For your consideration: > > Celebrating Crystalllography — a short film made by the Royal Institution > (in cahoots with production company 12foot6) and funded by the STFC. > > http://richannel.org/celebrating-crystallography > > ------------------------------ > > Date: Sat, 12 Oct 2013 17:16:43 +0530 > From: Dilip Badjugar <[log in to unmask]> > Subject: Rfree stuck > > Hello Experts, > > > I am trying to solve structure of a protein (213 a.a) complexed with a > peptide (14mer) using molecular replacement method. The complex crystals > are diffracted around 1.7 A and data is processed in p3(2)21 space group. > The structure was solved using apo protein with good LLG -3148 and TFZ > score- 49. The modeis refined in phenix the Rfactor -26.0 and Rfree is > 28.0. I have added ligand molecule in positive density and also added water > molecules (200), followed TLS refinement but still the Rfactor not came > down much ( Rfactor-21.53 and Rfree-25.44). There no outliers in > Ramachandran plot and most of the residues (97.21) are favored region. Can > you please suggest, what can be done to reduce the Rfree? > > Thanking you in advance. > DCB > > -- > Mr.Dilip C. Badgujar, > Senior Research Fellow, > ACTREC, > Tata Memorial Center, > Sector-22, Kharghar, > Navi Mumbai. > Pin-410210 > > ------------------------------ > > Date: Sat, 12 Oct 2013 14:11:29 +0200 > From: Tim Gruene <[log in to unmask]> > Subject: Re: Rfree stuck > > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Dear DCB, > > do not look at the R-values too much, look at your structure and your > maps. If they look as though you cannot improve the model any further, > accept that the R1/Rfree are 21% and 25% - at 1.7A resolution these > values are acceptable. Go publish this structure! > > If you do worry, remove the ligand, refine and check if the ligand > density comes back. That's a good control and probably the part of > your structure you are interested in. > > Best, > Tim > > On 10/12/2013 01:46 PM, Dilip Badjugar wrote: > > Hello Experts, > > > > > > I am trying to solve structure of a protein (213 a.a) complexed > > with a peptide (14mer) using molecular replacement method. The > > complex crystals are diffracted around 1.7 A and data is processed > > in p3(2)21 space group. The structure was solved using apo protein > > with good LLG -3148 and TFZ score- 49. The modeis refined in phenix > > the Rfactor -26.0 and Rfree is 28.0. I have added ligand molecule > > in positive density and also added water molecules (200), followed > > TLS refinement but still the Rfactor not came down much ( > > Rfactor-21.53 and Rfree-25.44). There no outliers in Ramachandran > > plot and most of the residues (97.21) are favored region. Can you > > please suggest, what can be done to reduce the Rfree? > > > > Thanking you in advance. DCB > > > > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.14 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > iD8DBQFSWTxxUxlJ7aRr7hoRAiKxAJ9NEVMhxKOwagl4XkiOc/UUiPihZACfZrHx > YzLCZjbw+po1Z8i2vKEHXQE= > =pYsk > -----END PGP SIGNATURE----- > > ------------------------------ > > End of CCP4BB Digest - 11 Oct 2013 to 12 Oct 2013 (#2013-289) > ************************************************************* >