The MFA applied to the methyl group data was similar to the one applied to backbone NH (Lakomek et al. 2008a, 2006). However, important modifications were required to account for the different properties of the methyl groups and are laid out here. A summary of the entire approach is illustrated in Fig. 1.
Fig. 1 Schematics of the approach used to obtain model-free parameters for methyl groups in ubiquitin. A total of m methyl group CH RDCs are measured in i alignment conditions. The homogeneity of these alignment conditions is analyzed by SECONDA (Hus and Brüschweiler 2002; Hus et al. 2003). Since methyl groups undergo rapid axial reorientation (<fs) about the adjacent CC bond, RDCs are scaled down to the corresponding CCmet RDCs. For each alignment medium i, a tensor is obtained from HN RDCs using the SCRM approach (Lakomek et al. 2008a). The tensors are scaled to CC RDCs and combined into the F matrix, which is then inverted to solve the dynamically averaged spherical harmonics <Y2,M> for each residue. All reported order parameters represent the axial motion of the CC bond