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Re: [ccp4bb] Fwd: [ccp4bb] X-Ray versus NMR Structure |
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CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999Subject: Re: Fwd: X-Ray versus NMR Structure From: mesters mesters {- at -} BIOCHEM {- dot -} UNI-LUEBECK {- dot -} DE Date: 2008-11-17 Charlie, This is not a good comparison because combining NMR and X-ray data is like having higher resolution again (i.e. more constraints). Further, the informations are much more of a "redundant nature" than "profoundly complementary" as they stem from the same molecule. More resolution would be "profoundly complementary"..... In my eyes the following statement still is true: ........ it is invariably the case that high resolution X-ray structures (< 2.0 Å) show significantly better agreement with solution observables such as coupling constants etc., that the corresponding NMR structures, including the very best ones........ Kuszewski, Gronenborn & Clore, Prot Sci 5, 1067-1080 (1996) - Jeroen - Charles W. Carter Jr. wrote: > > > Begin forwarded message: > >> *From: *"Charles W. Carter Jr." >> >> *Date: *November 15, 2008 9:51:36 AM EST >> *To: *Boaz Shaanan >> *Subject: **Re: [ccp4bb] X-Ray versus NMR Structure* >> >> Boaz: >> >> I have always and still fee that this paper is a landmark, because it >> shows that neither the X-ray nor the NMR data set alone gave as good >> a set of constraints for refinement as did both sets of constraints >> together. The structure that fitted both constraints ultimately gave >> a better fit to the NMR constraints AND to the crystallographic >> constraints than any of the models constrained only to one or the >> other set of constraints. Thus, the NOE distance constraints and the >> X-ray amplitudes are profoundly complementary. >> >> I formed that conclusion back in 92, when the paper was published, >> and have seen no evidence since that my conclusion then was wrong. >> >> Charlie >> >> >> On Nov 14, 2008, at 6:13 PM, Boaz Shaanan wrote: >> >>> oops, I forgot to give the reference: >>> >>> Science (1992), vol. 257, p. 961 >>> >>> Boaz >>> >>> ----- Original Message ----- >>> From: Young-Tae Lee >>> Date: Friday, November 14, 2008 23:57 >>> Subject: Re: [ccp4bb] X-Ray versus NMR Structure >>> To: CCP4BB@JISCMAIL.AC.UK >>> >>> > 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: dchen@caltech.edu >>> > > ********************************************** >>> > >>> > 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 >>> >>> ‎ >> >> **********UNCrystallographers NOTE new website url****************** >> carter@med.unc.edu >> http://xtal.med.unc.edu/CARTER/Welcome.html >> Department of Biochemistry and Biophysics CB 7260 >> UNC Chapel Hill, Chapel Hill, NC 27599-7260 >> Tel: 919 966-3263 >> FAX 919 966-2852 >> >> > > **********UNCrystallographers NOTE new website url****************** > > carter@med.unc.edu > > http://xtal.med.unc.edu/CARTER/Welcome.html > > Department of Biochemistry and Biophysics CB 7260 > > UNC Chapel Hill, Chapel Hill, NC 27599-7260 > > Tel: 919 966-3263 > > FAX 919 966-2852 > > > -- Dr. Jeroen R. Mesters Gruppenleiter Strukturelle Neurobiologie und Kristallogenese Institut für Biochemie, Universität zu Lübeck Zentrum für Medizinische Struktur- und Zellbiologie Ratzeburger Allee 160, D-23538 Lübeck Tel: +49-451-5004065, Fax: +49-451-5004068 Http://www.biochem.uni-luebeck.de Http://www.iobcr.org Http://www.selfish-brain.org Http://www.opticryst.org -- If you can look into the seeds of time and say which grain will grow and which will not - speak then to me (Macbeth) -- CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
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