We have developed an on-line NMR/X-ray Structure Pair Data Repository. The NIGMS Protein Structure Initiative (PSI) has provided many valuable reagents, 3D structures, and technologies for structural biology. The Northeast Structural Genomics Consortium was one of several PSI centers. NESG used both X-ray crystallography and NMR spectroscopy for protein structure determination. A key goal of the PSI was to provide experimental structures for at least one representative of each of hundreds of targeted protein domain families. In some cases, structures for identical (or nearly identical) constructs were determined by both NMR and X-ray crystallography. NMR spectroscopy and X-ray diffraction data for 41 of these NMR/X-ray structure pairs determined using conventional triple-resonance NMR methods with extensive sidechain resonance assignments have been organized in an on-line NMR/X-ray Structure Pair Data Repository. In addition, several NMR data sets for perdeuterated, methyl-protonated protein samples are included in this repository. As an example of the utility of this repository, these data were used to revisit questions about the precision and accuracy of protein NMR structures first outlined by Levy and co-workers several years ago [Andrec M, Snyder DA, Zhou Z, Young J, Montelione GT, Levy, R. (2007) PROTEINS 69: 449 465]. These results demonstrate that the agreement between NMR and X-ray crystal structures is improved using modern methods of protein NMR spectroscopy. The NMR/X-ray Structure Pair Data Repository will provide a valuable resource for new computational NMR methods development. This article is protected by copyright. All rights reserved.
[Question from NMRWiki Q&A forum] NMR Vs X ray crystal data not matching each other
NMR Vs X ray crystal data not matching each other
I had a very weird situation where my compound shows double bond between carbons in NMR but shows it as single bond in x ray data. Also my Mass spectrum agrees with NMR data and shows it as double bond. If these are single bond, i should see two more hydrogen weight added to mass but i do not see it in mass spec. Somebody please help if there could be an error in x ray software to identify a double bond in complex structure like morphine ?
Thanks much.
Check if somebody has answered this question on NMRWiki QA forum
High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data
High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data
Abstract X-ray diffraction and nuclear magnetic resonance spectroscopy (NMR) are the staple methods for revealing atomic structures of proteins. Since crystals of biomolecular assemblies and membrane proteins often diffract weakly and such large systems encroach upon the molecular tumbling limit of solution NMR, new methods are essential to extend structures of such systems to high resolution. Here we present a method that incorporates solid-state NMR restraints alongside...
nmrlearner
Journal club
0
09-26-2011 06:42 AM
High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data.
High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data.
High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data.
J Biomol NMR. 2011 Sep 22;
Authors: Tang M, Sperling LJ, Berthold DA, Schwieters CD, Nesbitt AE, Nieuwkoop AJ, Gennis RB, Rienstra CM
Abstract
X-ray diffraction and nuclear magnetic resonance spectroscopy (NMR) are the staple methods for revealing atomic structures of proteins. Since crystals of biomolecular...
nmrlearner
Journal club
0
09-23-2011 05:30 PM
CoNSEnsX: an ensemble view of protein structures and NMR-derived experimental data.
CoNSEnsX: an ensemble view of protein structures and NMR-derived experimental data.
Related Articles CoNSEnsX: an ensemble view of protein structures and NMR-derived experimental data.
BMC Struct Biol. 2010 Oct 29;10(1):39
Authors: Angyan AF, Szappanos B, Perczel A, Gaspari Z
ABSTRACT: BACKGROUND: In conjunction with the recognition of the functional role of internal dynamics of proteins at various timescales, there is an emerging use of dynamic structural ensembles instead of individual conformers. These ensembles are usually substantially...
nmrlearner
Journal club
0
11-03-2010 10:44 AM
CoNSEnsX: an ensemble view of protein structures and NMR-derived experimental data -
CoNSEnsX: an ensemble view of protein structures and NMR-derived experimental data - 7thSpace Interactive (press release)
<img alt="" height="1" width="1" />
CoNSEnsX: an ensemble view of protein structures and NMR-derived experimental data
7thSpace Interactive (press release)
These ensembles are usually substantially more diverse than conventional NMR ensembles and eliminate the expectation that a single conformer should fulfill ...
Read here
nmrlearner
Online News
0
10-29-2010 09:32 PM
[NMRwiki tweet] nmrwiki: Software to calculate theoretical second moment from crystal structure data?
nmrwiki: Software to calculate theoretical second moment from crystal structure data?http://qa.nmrwiki.org/question/180/
nmrwiki: Software to calculate theoretical second moment from crystal structure data?http://qa.nmrwiki.org/question/180/
Source: NMRWiki tweets
nmrlearner
Twitter NMR
0
09-29-2010 10:24 AM
[Question from NMRWiki Q&A forum] Free program to calculate the theoretical second moment from crystal structure data?
Free program to calculate the theoretical second moment from crystal structure data?
Does anyone know of a free, available program I can use to calculate the theoretical second moment from crystal structure data? I was only able to find one online, written in a mix of FORTRAN 77/90. The current limitations of the program can't accommodate my system (big unit cell and lots of atoms), and FORTRAN coding really isn't my fortay.
Ideally, the program would be able to simulate second moment(s) by defining specific rotational axes, and modeling different rotational rates and hopping angles...
A Community Resource of Experimental Data for NMR X-ray Crystal Structure Pairs
Linear Mode
