>Many NMR structures are more modelled than experimentally determined,
>the number of independent experimental
>data can be quite small. But the good news is that force fields and
>modelling software are improving.
>George
The quality of NMR structures/models depend heavily on the number of experimental NOE distance restraints per residue. Naturally, for inner core, stable regions of the protein this number is quite high (10 NOE or more per residue) but for flexible regions it's (very) low with NOEs possibly missing altogether in such regions. The model derived from NMR data suffer from similar problems that the crystal structures do. Crystal structures yield good looking density, low B's in ordered regions, bad looking density, sometime even missing density altogether and very high B in flexible regions. The NMR equivalent would be good superposition of the models in ordered regions and bad superposition (shown as a pile of noodle in NMR models) in flexible regions. This is also expressed in the rmsd column of PDBs from NMR models. As for the 'resolution' of NMR models - this is a debatable question. Some NMR people claim that a good NMR structure with 10 NOE/residue is equivalent to ~2A resolution structure. Maybe.
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
E-mail: [log in to unmask]
Phone: 972-8-647-2220 Skype: boaz.shaanan
Fax: 972-8-647-2992 or 972-8-646-1710
On 06/09/2013 08:12 PM, Ethan Merritt wrote:
> On Sunday, 09 June 2013, Theresa Hsu wrote:
>> Dear all
>>
>> A question for the cross-trained members of this forum - for small sized proteins, is NMR better than crystallography in terms of data collection (having crystals in the first place) and data processing? How about membrane proteins?
> A relevant study is the comparison by Yee et al (2005) JACS 127:16512.
> <http://pubs.acs.org/doi/abs/10.1021/ja053565+>
>
> They tried to solve 263 small proteins using both NMR and crystallography.
> 43 only worked for NMR
> 43 only worked for X-ray
> 21 could be solved either way
>
> So you could say it was a toss-up, but consider that
> - As the size gets larger, NMR becomes increasingly impractical
> - 156 (60%) weren't solved by either NMR or crystallography.
> What is the relative cost of the failed attempt?
>
> Ethan
>
--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582
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