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
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)
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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
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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
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Date: Sat, 12 Oct 2013 14:11:29 +0200
From: Tim Gruene <[log in to unmask]>
Subject: Re: Rfree stuck
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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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End of CCP4BB Digest - 11 Oct 2013 to 12 Oct 2013 (#2013-289)
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