Here are some of my thoughts and I was also seeking good references
pointing out systematic comparison of X-ray and NMR approaches.
Both X-ray and NMR structures are models calculated from experimental
data. Therefore coordinates from both structures have uncertainty and
are inevitably somehow biased.
B-factors of crystal structural models would contain that uncertainty
information. Crystal structures with low resolution data will have
higher uncertainty contribution to B-factors than high resolution
structures.
Note that NMR structures are typically represented as ensembles. This
is largely because of limited number of experimental data for
accurate determination of structures. Traditionally many starting
structures are calculated to fulfill interatomic distances derived
from NMR experimental data. A set of converged structures are refined
further as in x-ray structure refinement.
Pairwise RMSD of ensemble indicates the precision of NMR structures.
As more number of NMR data is used for calculation, resultant RMSD of
ensemble is smaller, indicating more precise structures, but not
necessarily more accurate structures. Different from X-ray
crystallography, there is not very good way to assess accuracy of NMR
structures. However, as many restraints are added, contribution of
wrong restraints becomes smaller or could be excluded during
calculation.
RMSD of ensemble of NMR structures can be interpreted as the
uncertainty of coordinates. Core residues of NMR structures have
smaller RMSDs in a similar way that core residues of crystal
structures have relatively smaller B-factors compared to surface
residues.
3A crystal structure would have 1A displacement of atoms in average
calculated from B-factors. The precision of this resolution crystal
structure could correspond to that of NMR ensemble with 1A pairwise
RMSD. For another example, NMR ensemble with 0.4A RMSD will have a
similar precision to 1.4A crystal structure.
Both x-ray and NMR approaches can reveal "atomic resolution
structures" but precision and quality of structures should be varying
depending on individual examples.
Finally, incorporation of uncertainty in explicit way for crystal
structures as for NMR ensemble could be useful for better
representation of structural models as shown in the following paper.
Ensemble Refinement of Protein Crystal Structures: Validation and
Application, Structure 15, 1040-1052, 2007
Young-Tae
On Nov 13, 2008, at 8:57 PM, David Chenoweth wrote:
Dear all,
Does anyone know of a good published reference that describes the
pros and cons of X-ray versus NMR structure determination.
Something specific to nucleic acids would even be better. I've
noticed that several papers describe NMR structures as "atomic
resolution structures" and I'm just wondering what people think of
this.
Thanks in advance,
David
**********************************************
David M. Chenoweth
California Institute of Technology
Division of Chemistry and Chemical Engineering
Mail Code: 164-30
1200 California Boulevard, 91125 Pasadena
California, USA
Phone: 626-395-6074
Email: [EMAIL PROTECTED]
**********************************************
Young-Tae Lee, Ph. D.
Research Associate
The Scripps Research Institute
Dept. of Molecular Biology
