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Lars Andersen Bratholm edited In_the_case_of_GB3__.tex
over 8 years ago
Commit id: 706f325007a1d667abcf524b831cd7174dd24063
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In the case of GB3 the RMSD ($r$) value for C$\beta$ can be reduced (increased) to 1.8 ppm (0.71) by removing a single outlier identified by the Generalized Extreme Studentized Deviate Test. The outlier is Ala20 for which ProCS15 and DFT predict a C$\beta$ chemical shielding value of
177.4 176.8 and 167.4 ppm, respectively. Inspection of the structure shows that the C$\beta$ atom is only 3.1 Å from the N atom of Ala26 - an interaction not taken into account in the parameterization of ProCS15.
Similarly (also for GB3), the RMSD ($r$) value for H can be reduced (increased) to 0.6 ppm (0.91) by removing a single outlier identified by the Generalized Extreme Studentized Deviate Test. The outlier is Gln2 for which ProCS15 and DFT predict a C$\beta$ chemical shielding value of 25.0 and 20.1 ppm, respectively. Inspection of the structure shows that the H$^\text{N}$ atom is within 1.77 Å of the OE1 atom of the Gln side chain and with 2.54 Å of an H$\varepsilon$ atom of the Met1 side chain. While the former interaction should be included in the $\sigma_{BB}^{i-1}$ term, the latter interaction is not and may be responsible for the large deviation. This residue is also identified as an outlier for N and removing it reduces (increases) the RMSD ($r$) value to 4.0 ppm (0.88).
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