Weight: Chi1 and Chi2 adopt favored conformations based on data from X-ray crystallography (Guo Z, Cascio D, Hideg K, Hubbell WL Protein Sci 2008;17:228-239) In PRONOX, the calculated inter-label distance is biased to reflect a greater representation of the favored conformers in each label distribution. A weighting of 0.9 means that in the calculation of the average distance, an inter-label distance between two favorable conformers is multiplied by 0.81 (0.9 × 0.9), a distance between a favorable and an unfavorable conformer is multiplied by 0.09 (0.9 × 0.1), and a distance between two unfavorable conformers is multiplied by 0.01 (0.1 × 0.1).
Glycine: To label at a glycine in the original protein, make sure that the H atom position to be modified is named '3HA ' (this is the AMBER naming system) or ' HA3'. Care should be taken that the correct label chirality is obtained.
Fine Search: The “fine search” option can be activated for a label position for which conformers cannot be obtained using the standard conditions. In this approach, a fine search over the local conformational space is performed, with any of the chosen torsion angles varied systematically as the original torsion angle (t) – 0.2*increment (I); t – 0.1*I; t; t + 0.1*I; and t + 0.2*I. If any conformer in the fine search meets the above criterion for acceptance, the original conformer is used in the inter-label distance calculation.