Table 2. Summary of NOE distances violation and energy penalties for the DDD sequence using the NMR data obtained in-house (see ‘Materials and Methods’ section)a.
Structure | N° of violations | Energy penaltyb (kcal/mol) | Average violation (Å) | Largest violation (Å) |
---|---|---|---|---|
BSC1-NOE | 8 | 20.4 | 0.35 | 0.46 |
BSC0-NOE | 9 | 22.7 | 0.35 | 0.43 |
BSC0OL15-NOE | 14 | 35.0 | 0.35 | 0.47 |
Standard NMR | 5 | 11.3 | 0.33 | 0.40 |
1NAJc | 35 | 159.2 | 0.47 | 0.63 |
1GIPc | 50 | 265.4 | 0.51 | 1.06 |
X-RAYc | 46 | 332.1 | 0.60 | 1.58 |
aTaking T as 298.15 K, the kT constant has a value of 0.5924812 kcal mol−1. We considered an experimental restraint violated when its average penalty energy was above 3·kT. Given the force constant used to apply the distance restraints (kres = 20 kcal/Å2), 3·kT is equivalent to set a tolerance of ±0.3 Å on the experimental range to consider that a specific distance has been violated.
bFor each distance the energy penalty (Epen) was computed as: Epen = kres(distcalc-distobs)2. Note that we simply reported the sum of each individual Epen.
cA single-point calculation in vacuo was performed on the average experimental structure applying our NMR restraints.