title: Complete cross-validation and R-factor calculation of a solid-state NMR derived structure.
abstract: Cross-validation of a solid-state NMR-derived membrane polypeptide structure is demonstrated. An initial structure has been achieved directly from solid-state NMR derived orientational restraints based on a variety of anisotropic nuclear spin interactions. Refining the molecular structure involves setting up a penalty function that incorporates all available solid-state NMR experimental data and an energy function. A validation method is required to choose the optimal weighting factor for the total penalty function to balance the contribution from the experimental restraints and the energy function. Complete cross-validation has been used to avoid over-fitting the orientational restraints. Such cross-validation involves partitioning of the experimental data into a test set and a working set followed by checking the free R-value during the refinement process. This approach is similar to the method used in crystallography and solution NMR. Optimizing the weighting factor on the penalty function by cross-validation will increase the quality of the refined structure from solid-state NMR data. The complete cross-validation and R-factor calculation is demonstrated using experimental solid-state NMR data from gramicidin A, a monovalent cation channel in lipid bilayers.
authors.affiliation: Center for Interdisciplinary Magnetic Resonance, National High Magnetic Field Laboratory (NHMFL), Institute of Molecular Biophysics, Department of Chemistry, and Department of Mathematics, Florida State University, Tallahassee, Florida 32310, USA.
authors.forename: S
authors.initials: S
authors.lastname: Kim
authors.forename: J R
authors.initials: JR
authors.lastname: Quine
authors.forename: T A
authors.initials: TA
authors.lastname: Cross