In a non-computational capacity would also suggest perhaps resequencing your clone. Occasionally the published sequences are off, the specific base is polymorphous or there is also the possibility that you introduced a mutation somewhere. That would be the cheap and easy way to definitively answer the question.
Cheers, Katherine On Thu, Dec 8, 2011 at 1:43 PM, Petr Leiman <petr.lei...@epfl.ch> wrote: > Dear Tim, > > I agree with you completely. The question then becomes why does the > automatic weighting scheme in refmac allow R and R-free to run away from > each other by 8% in a 1.1 A resolution structure? > > Petr > > On Dec 8, 2011, at 6:50 PM, Tim Gruene wrote: > > > -----BEGIN PGP SIGNED MESSAGE----- > > Hash: SHA1 > > > > Dear Christopher, > > > > if your R/Rfree from Refmac5 really are 10% vs. 18%, you might simply be > > looking at an electron density map with strong model bias, i.e. the map > > shows the features of the model and not of the data. Although at 1.1A > > resolution this seems quite unlikely, but that's what might explain this > > great gap between R and Rfree. > > > > Tim > > > > On 12/08/2011 06:36 PM, Christopher Browning wrote: > >> Dear All, > >> > >> Question: Has anybody ever refined the same structure using PHENIX and > >> then tried REFMAC to see what happens? > >> > >> I did and I stumbled on something funny. I'm refining a structure at > >> 1.1A resolution which was solved with Iodine phasing using PHENIX > >> AutoSolve. Got a great map and the structure was built almost > >> completely. I had to build a few residues myself, and using the > >> published sequence, I started filling in the residues, but as I came > >> nearer the N-terminus, it looked like the density did not match residues > >> from the sequence. I kept the residues as in the sequence, but as you > >> can see from the PHENIX refined picture (below is the link) it still > >> looks like the amino acid sequence in the crystal does not match the > >> published protein sequence. > >> > >> Out of interest I refined the same file in REFMAC, and now the electron > >> density is correct, and the sequence of the amino acids in the crystal > >> matches the published sequence (see link for picture below). Not only > >> that..... my R/Rfree improved (16.5/19 for PHENIX, 10/18 for REFMAC). > >> > >> I've also refined the occupancies of the iodide, however the the output > >> FO-FC map from PHENIX complains and the REFMAC map is fine..... > >> > >> How can this be and what causes this? > >> > >> Link for the pictures: > >> Both maps are at identical Sigma levels in both pictures. > >> PHENIX: http://dl.dropbox.com/u/51868657/PHENIX_refined.png > >> REFMAC: http://dl.dropbox.com/u/51868657/REFMAC_refined.png > >> > >> Cheers, > >> > >> Chris Browning > >> > >> > >> > > > > - -- > > Dr Tim Gruene > > Institut fuer anorganische Chemie > > Tammannstr. 4 > > D-37077 Goettingen > > > > GPG Key ID = A46BEE1A > > -----BEGIN PGP SIGNATURE----- > > Version: GnuPG v1.4.10 (GNU/Linux) > > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > > > iD8DBQFO4PjgUxlJ7aRr7hoRAszXAKCNmTZvCVaDUm6v3lQjp051H+ilDgCgxd1l > > as9CcWEseq9uEV8qMZsOfsg= > > =KKUr > > -----END PGP SIGNATURE----- >
