Quick navigation: Home   |    Site Map   ||    References   |    Biography   ||    Copyright   |    Other copyright   |    Contact us   |    Advert   |   
 

Re: [ccp4bb] X-Ray versus NMR Structure
- Protein crystallography

Main steps:

   - Protein purification
   - Crystallisation

Special:

   - Programs for crystallography
   - X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

   - CCP4BB

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999
Previous message:
Subject: Re: X-Ray versus NMR Structure
From: Boaz Shaanan bshaanan {- at -} BGU {- dot -} AC {- dot -} IL
Date: 2008-11-14		Next message:
Subject: Re: off-topic: soft crystals?
From: deliang deliangc {- at -} UCI {- dot -} EDU
Date: 2008-11-14


Subject: Re: X-Ray versus NMR Structure
From: Boaz Shaanan bshaanan {- at -} BGU {- dot -} AC {- dot -} IL
Date: 2008-11-14

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
ProteinCrystallography.org: Copyright 2006-2010 by Quid United Ltd