Re: [ccp4bb] an over refined structure

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: an over refined structure
From: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2008-02-04

Next message:
Subject: Re: an over refined structure
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2008-02-04

Subject: Re: an over refined structure
From: Sun Tang suntang2222 {- at -} YAHOO {- dot -} COM
Date: 2008-02-04

Hi Tim,

Thank you for your and information and suggestions. There are two indepdent molecules in the asymmetric unit and one molecule does not have very good density, especially in the N-terminus.

Do you think that I should remove the region in the refinement?

Best,

Sun

Tim Gruene wrote: I would agree that the difference is suspiciously high. I. Tickle and
others have published analytical expressions for how to estimate the ratio
between R and Rfree, just google for "tickle rfree" to find the
references.

You easily achieve a large difference by adding too many waters which just
model noise. There may be other reasons for which more knowledge about the
structure is required. Do you have large unmodelled regions, like loops
that do not show in the density map?

Tim

--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

On Mon, 4 Feb 2008, Sun Tang wrote:

> Hello All,
>
> I refined a structure with Refmac in CCP4i and the R/Rfree is 0.215/0.277. The difference between R and Rfree is too much even though I used 0.01 for weighting term in the refinement (the default value is 0.3). The RMSD for bond length and bond angle is 0.016 A and 1.7 degree.
>
> What may be wrong with the over-refined structure? What is the reason for leading to an over-refined structure? How to avoid it?
>
> Best wishes,
>
> Sun Tang
>
>
> ---------------------------------
> Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now.

---------------------------------
Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now.

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: an over refined structure
From: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2008-02-04

Next message:
Subject: Re: an over refined structure
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2008-02-04