Open AccessSimultaneous use of solution NMR and X‐ray data in REFMAC 5 for joint refinement/detection of structural differences
Author(s) -
Rinaldelli Mauro,
Ravera Enrico,
Calderone Vito,
Parigi Giacomo,
Murshudov Garib N.,
Luchinat Claudio
Publication year - 2014
Publication title -
acta crystallographica section d
Language(s) - English
Resource type - Journals
ISSN - 1399-0047
DOI - 10.1107/s1399004713034160
Subject(s) - crystallography , chemistry , residual dipolar coupling , paramagnetism , molecule , orientation (vector space) , diamagnetism , calmodulin , solid state nuclear magnetic resonance , biological system , materials science , nuclear magnetic resonance spectroscopy , nuclear magnetic resonance , physics , mathematics , stereochemistry , condensed matter physics , geometry , organic chemistry , quantum mechanics , magnetic field , calcium , biology
The program REFMAC 5 from CCP 4 was modified to allow the simultaneous use of X‐ray crystallographic data and paramagnetic NMR data (pseudocontact shifts and self‐orientation residual dipolar couplings) and/or diamagnetic residual dipolar couplings. Incorporation of these long‐range NMR restraints in REFMAC 5 can reveal differences between solid‐state and solution conformations of molecules or, in their absence, can be used together with X‐ray crystallographic data for structural refinement. Since NMR and X‐ray data are complementary, when a single structure is consistent with both sets of data and still maintains reasonably `ideal' geometries, the reliability of the derived atomic model is expected to increase. The program was tested on five different proteins: the catalytic domain of matrix metalloproteinase 1, GB3, ubiquitin, free calmodulin and calmodulin complexed with a peptide. In some cases the joint refinement produced a single model consistent with both sets of observations, while in other cases it indicated, outside the experimental uncertainty, the presence of different protein conformations in solution and in the solid state.