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. 2009 Nov 26;38(3):e18. doi: 10.1093/nar/gkp1061

Table 1.

NMR experimental observables compared to their simulated counterpart

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.