If we find that the best estimate of RMSD bonds for structures at
atomic resolution (where prior restraints do not have much effect) is
002 we can believe, cant we, that this a property of protein structures
- ie some bonds are distorted by the protein environment and the Xray
model illustrates this. (Bioinformaticists can and do analyse which
types of bond, in which environment, show the greates distortions...)
And I would expect that the nature of the protein folded structure is
more or less independent of the qualiy of the crystal it forms..
So doesnt it follow that you should get more or less the same RMSD for
the geometry for structures refined at any resolution? Tassos's example
fits in with that too..
All this assumes that you have built the structures correctly and of
course you are much more likely to have made errors at 3A than at 1A.
But tightening or loosening the restraints will not correct them.. So
for initial builds, I often think it is sensible to release restraints
on both B factors and bond lengths, then look for wild outliers - they
often flag the dodgey regions.
Eleanor
Anastassis Perrakis wrote:
On Aug 23, 2006, at 9:59, Clemens Vonrhein wrote:
But what should be those values? I guess at 1A resolution I'd expect a
rmsd(bond) of 0.02 or larger. And at 3.5A I'd expect a rmsd(bond) of
0.005 or smaller. But these are personal choices (same as I/sig(I)
or Rmerge cut-offs in data-reduction).
But maybe I'm completely wrong here ... correct me please?
Although i think Clemens is very far from being wrong, as usual, I
cant help
contributing another set of personal choices and a brief justification.
Most important, and as Clemens explains, RMSD on bond lengths
and standard deviation of the Engh&Huber distributions, are different
things.
However, there must be some correlation: if (to exaggerate) a certain
type of bond is
in the dictionary 1.0 +/- 0.1 A, I would doubt if it makes sense to
restrain it in a way that
the deviation of the distribution of this type of bonds in a 3.5
A structure is 1.0 +/- 0.001.
Thats just intuition and I have a concern that this is one of the
things that intuition serves
you wrong and statistics would say otherwise. But, i would be curious
to see why this is
wrong/right. I will go and read the Cruickshank paper that Dirk
pointed out to us ...
I also think that beside personal preferences, Rfree would have one or
two things to say here.
Should we simply aim for an RMSD between 0.005-0.020, that also gives
minimal Rfree ?
I did a quick experiment with our current favorite nightmare at 3.3 A
resolution, 360 residues, no NCS.
I am reporting the achieved RMSD, the Rfree and the number of residues
flagged by procheck as Rama outliers. The model I started with is
'towards the end' and had an initial 'original' rmsd of about 0.016
when I started this test.
RMSD Rfree Nres
0.020 31.2 31
0.016 31.3 27
0.010 31.4 23
0.007 31.9 20
0.005 32.2 22
from that I would say, that - for our structure - the middle job is
best: i would expect that after quickly fixing 4-5 residues in the
graphics and running a job that would give an RMSD about 0.015 to be
the best at the end. But, of course now I am tempted to take the 0.007
model, look at it, and then slowly 'release it' towards the end. ;-)
Having said these I want to iterate one point that was made:
Use hydrogens. It can only help and it costs nothing.
And to make a new point: use TLS.
The major reason that some crystals do not diffract at high enough
resolution,
should be rigid body motions and TLS describes exactly that, while being
very 'cheap' in parameters, so use it. for the above structure is
makes a huge
difference.
btw: i found torsional refinement as implemented in CNS not useful
compared with refmac5 / phenix or Buster. I was a bit surprised by
that, but ...
A.
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