In addition to bulk solvent, the other well recognized problem with
macromolecular structures is the inadequate description of disorder.
With small molecules, the Debye-Waller works much better because the
harmonic oscillator is indeed a good model there. Note that the problem
is not anisotropy (which we can model if resolution is sufficiently
high), but rather anharmonic motion and multiple conformations that go
undetected.
On Thu, 2010-10-28 at 08:00 -0500, Jacob Keller wrote:
> So I guess a consequence of what you say is that since in cases where there
> is no solvent the R values are often better than the precision of the actual
> measurements (never true with macromolecular crystals involving solvent),
> perhaps our real problem might be modelling solvent?
> Alternatively/additionally, I wonder whether there also might be more
> variability molecule-to-molecule in proteins, which we may not model well
> either.
>
> JPK
>
> ----- Original Message -----
> From: "George M. Sheldrick" <[log in to unmask]>
> To: <[log in to unmask]>
> Sent: Thursday, October 28, 2010 4:05 AM
> Subject: Re: [ccp4bb] Against Method (R)
>
>
> > It is instructive to look at what happens for small molecules where
> > there is often no solvent to worry about. They are often refined
> > using SHELXL, which does indeed print out the weighted R-value based
> > on intensities (wR2), the conventional unweighted R-value R1 (based
> > on F) and <sigmaI>/<I>, which it calls R(sigma). For well-behaved
> > crystals R1 is in the range 1-5% and R(merge) (based on intensities)
> > is in the range 3-9%. As you suggest, 0.5*R(sigma) could be regarded
> > as the lower attainable limit for R1 and this is indeed the case in
> > practice (the factor 0.5 approximately converts from I to F). Rpim
> > gives similar results to R(sigma), both attempt to measure the
> > precision of the MERGED data, which are what one is refining against.
> >
> > George
> >
> > Prof. George M. Sheldrick FRS
> > Dept. Structural Chemistry,
> > University of Goettingen,
> > Tammannstr. 4,
> > D37077 Goettingen, Germany
> > Tel. +49-551-39-3021 or -3068
> > Fax. +49-551-39-22582
> >
> >
> > On Wed, 27 Oct 2010, Ed Pozharski wrote:
> >
> >> On Tue, 2010-10-26 at 21:16 +0100, Frank von Delft wrote:
> >> > the errors in our measurements apparently have no
> >> > bearing whatsoever on the errors in our models
> >>
> >> This would mean there is no point trying to get better crystals, right?
> >> Or am I also wrong to assume that the dataset with higher I/sigma in the
> >> highest resolution shell will give me a better model?
> >>
> >> On a related point - why is Rmerge considered to be the limiting value
> >> for the R? Isn't Rmerge a poorly defined measure itself that
> >> deteriorates at least in some circumstances (e.g. increased redundancy)?
> >> Specifically, shouldn't "ideal" R approximate 0.5*<sigmaI>/<I>?
> >>
> >> Cheers,
> >>
> >> Ed.
> >>
> >>
> >>
> >> --
> >> "I'd jump in myself, if I weren't so good at whistling."
> >> Julian, King of Lemurs
> >>
> >>
>
>
> *******************************************
> Jacob Pearson Keller
> Northwestern University
> Medical Scientist Training Program
> Dallos Laboratory
> F. Searle 1-240
> 2240 Campus Drive
> Evanston IL 60208
> lab: 847.491.2438
> cel: 773.608.9185
> email: [log in to unmask]
> *******************************************
--
"I'd jump in myself, if I weren't so good at whistling."
Julian, King of Lemurs
|