Re: [ccp4bb] Antw: Re: [ccp4bb] What are acceptable Rwork/Rfree for publication

[Eleanor Dodson]

The R factors may be high because the structure is imperfect - almost
inevitable at that resolution - but also there are often serious
difficulties with scaling at this resolution . If you are using REFMAC look
at the  v  wrt resolution plot at the end of refinement (follows R
and Rfree plot v resolution 0. You may see there is a large discrepancy..
Never sure what to do about it - the higher resolution data you can use the
more reliable the scaling so maybe you can extend the resolution by
accepting CC1/2 < 0.5 or whatever your data cut off is based on..
REFMAC offers various scaling options, trying to deal with the bulk
solvent.

But maybe your scaling is OK - just check it as a matter of course!1

Eleanor



On 14 June 2017 at 15:32, Matthias Barone  wrote:

> If you dont use Phenix, print the figures of
> https://doi.org/10.1016/S0969-2126(02)00743-8
> and use them beside your screen. Helps a lot if you wanna have a quick
> look at Rfact distributions..
>
>
> >>> Paul Emsley  14.06.17 15.25 Uhr >>>
> On 14/06/2017 14:09, Khoa Pham wrote:
> > Dear CCP4 members,
> >
> > I am refining a structure with a resolution of ~ 2.9 A and the
> Rwork/Rfree are are
> > 0.34/0.37, respectively.
> > My question is that these Rwork/Rfree are acceptable for publication.
>
> If you have Phenix, try POLYGON. That will give you a good clue.
>
> >If not, how can I
> > reduce them?
> >
>
> That is more complicated to answer.
>
>
> Paul.
>

[ccp4bb] Antw: Re: [ccp4bb] What are acceptable Rwork/Rfree for publication

[Matthias Barone]

If you dont use Phenix, print the figures of 
https://doi.org/10.1016/S0969-2126(02)00743-8
and use them beside your screen. Helps a lot if you wanna have a quick look at 
Rfact distributions..




>>> Paul Emsley  14.06.17 15.25 Uhr >>>
On 14/06/2017 14:09, Khoa Pham wrote:
> Dear CCP4 members,
> 
> I am refining a structure with a resolution of ~ 2.9 A and the Rwork/Rfree 
> are are 
> 0.34/0.37, respectively.
> My question is that these Rwork/Rfree are acceptable for publication. 

If you have Phenix, try POLYGON. That will give you a good clue.

 >If not, how can I
> reduce them?
> 

That is more complicated to answer.


Paul.