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." <[log in to unmask]
>> <mailto:[log in to unmask]>>
>> *Date: *November 15, 2008 9:51:36 AM EST
>> *To: *Boaz Shaanan <[log in to unmask] <mailto:[log in to unmask]>>
>> *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 <[log in to unmask] <mailto:[log in to unmask]>>
>>> Date: Friday, November 14, 2008 23:57
>>> Subject: Re: [ccp4bb] X-Ray versus NMR Structure
>>> To: [log in to unmask] <mailto:[log in to unmask]>
>>>
>>> > 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: [log in to unmask] <mailto:[log in to unmask]>
>>> > > **********************************************
>>> >
>>> > 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******************
>> [log in to unmask] <mailto:[log in to unmask]>
>> 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******************
>
> [log in to unmask] <mailto:[log in to unmask]>
>
> 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
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