Table 1.
MD_ref | MD_δP | ||
---|---|---|---|
ds(H2′) ds(H2′′) ds(H6/8) | R | 0.90 | 0.93 |
Δ_d | 0.3 | 0.3 | |
‘Other’ distances | R | 0.75 | 0.56 |
Δ_d | 0.35 | 0.5 | |
BII percentage | R | 0.70 | 0.93 |
RMSD | 21 | 15 |
Experimental NMR observables for the Jun-Fos oligomer include internucleotide distances measured from NOE spectra and the percentage of BII conformation for every phosphate. These observables are compared to their simulated counterpart, whether obtained with a conventional refinement protocol (MD_ref) or with the δP-based method (MD_δP). The NOE distances are divided into a group of distances restrained in the two MDs [ds(H2′), ds(H2′′) and ds(H6/8)] and the distances (‘Other’ distances) restrained in MD_ref but not in MD_δP. The correlation coefficients (R) and the average differences (Δ_d in Å) between NMR and simulated distances are given for each distance category, across MDs. The RMSD between the experimental and simulated BII percentages was calculated as: RMSD = [Σ(%BIItheo – %BIIexp)2 / N]½, with N = 22, number of phosphate. The best and worst values of the RMSD would be 0 and 100, respectively.