Hi, I don't know what you mean by a systematic comparison between NMR and X-ray structures, but in this paper from 1992 (maybe it's not good enough because it's more than 10 years old - according to a recent paper in Science, articles older than 10 years are referred to much less frequently than 'younger' articles), we showed that at around 2.0 A resolution, X-ray structures and good NMR structures (i.e. those that are based on a large number of NOE's) are comparable, provided they're treated properly. This is not at all surprising, since at this kind of resolution X-ray crystallographers and NMR people rely heavily on restraints in order to derive their models and even use the same programs (X-PLOR and CNS). When crystals diffract to higher resolution, the data weigh more heavily and differences between the models can be expected, let alone the fact that they reflect different situations (crystalline environment vs. solution). And of course, small molecules people don't need to rely on restraints at all in order to derive near perfect atomic models.
Cheers, Boaz ----- Original Message ----- From: Young-Tae Lee <[EMAIL PROTECTED]> Date: Friday, November 14, 2008 23:57 Subject: Re: [ccp4bb] X-Ray versus NMR Structure To: [email protected] > 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 > > > > Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan
