We have developed an online 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 online 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 coworkers several years ago (Andrec et al., Proteins 2007;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.
A Community Resource of Experimental Data for NMR – X-ray Crystal Structure Pairs
A Community Resource of Experimental Data for NMR – X-ray Crystal Structure Pairs
ABSTRACT
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...
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08-22-2015 11:20 AM
[NMR paper] A Community Resource of Experimental Data for NMR - X-ray Crystal Structure Pairs.
A Community Resource of Experimental Data for NMR - X-ray Crystal Structure Pairs.
Related Articles A Community Resource of Experimental Data for NMR - X-ray Crystal Structure Pairs.
Protein Sci. 2015 Aug 21;
Authors: Everett J, Tejero R, Murthy SB, Acton TB, Aramini JM, Baran MC, Benach J, Cort JR, Eletsky A, Forouhar F, Guan R, Kuzin AP, Lee HW, Liu G, Mani R, Mao B, Mills JL, Montelione AF, Pederson K, Powers R, Ramelot T, Rossi P, Seetharaman J, Snyder D, Swapna GV, Vorobiev SM, Wu Y, Xiao R, Yang Y, Arrowsmith CH, Hunt J, Kennedy MA, Prestegard...
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08-22-2015 11:20 AM
[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.
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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...
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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...
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09-23-2011 05:30 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
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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
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