PMC:2728246 / 14149-16080 JSONTXT

{"target":"http://pubannotation.org/docs/sourcedb/PMC/sourceid/2728246","sourcedb":"PMC","sourceid":"2728246","source_url":"https://www.ncbi.nlm.nih.gov/pmc/2728246","text":"Methyl groups are too mobile to reliably determine the alignment tensors of the F-matrix from their RDCs. It is also not possible to calculate the alignment tensor exclusively from the more rigid alanine side chains, since ubiquitin contains only two of them. However, for each alignment condition, a set of NH RDCs (1DNH) from the much more rigid backbone were also available. Thus, we have used the alignment tensor estimated from the backbone NH RDCs and applied a linear scaling to the principal component in alignment medium i to obtain . This conversion factor was estimated to:2 assuming NH and CCmet bond lengths corresponding to rNH = 1.04 Å and rCC = 1.53 Å. For the NH couplings, alignment tensors have been calculated using the software PALES (Zweckstetter and Bax 2000) applied to the dynamic average NH orientations obtained after four SCRM cycles for the NH RDC data set D36M, as described in (Lakomek et al. 2008a). Rhombicity and Eulerian angles were assumed to remain unchanged. The 20% most mobile NH residues as derived for datasets D36M were excluded from alignment tensor calculation in order to minimize the effect of alignment tensor fluctuations. Since only a dynamically reduced principal component of the alignment tensor can be derived from the dynamically averaged \u003cD(NH)\u003e, the static value of Di,zz has to be estimated using a robust statistical scaling method that is explained in detail in the supporting information of (Lakomek et al. 2008a). The same overall scaling factor has been used. We want to emphasize that only the order parameter is affected by the scaling factor. All other MF parameters (see below) are entirely unaffected by a change in the overall scaling. Also, the rotameric analysis (last section) is largely unaffected by a change in the scaling factor as long as this change can be compensated by adjusting the local order parameter for the fast fluctuations within a minimum.","divisions":[{"label":"label","span":{"begin":584,"end":585}}],"tracks":[]}