oops, I forgot to give the reference: Science (1992), vol. 257, p. 961
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
