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Table 5 Rule-based model parameters for three pen a 1 conformations

From: Extending rule-based methods to model molecular geometry and 3D model resolution

Parameter

Native

S-shaped

U-shaped

Cutoff distance (nm)

7.0–8.7

6.8–8.3

6.8–8.6

k f1 (molecule −1 s −1)

1.00

1.00

1.00

k f2 (molecule −1 s −1)

0.006595

0.003558

0.007315

k r (s −1)

0.01

0.01

0.01

σ

0.000703

0.000135

0.000469