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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
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