Root Mean Square Deviation (RMSD) analysis.

(A, B) Cross-correlation (Pearson correlation) of RMSD values of each domain for wild type and D170A variant. Here RMSD values were calculated with the first frame of reference since the correlation of dynamic changes of each domain is of interested. The cross-correlation was done by merging the rmsd of 6 copies trajectory together, and then the Pearson correlation among different domains were calculated. While worth being noted, the correlation value does not suggest the functional correlation between domains, since RMSD is an overall measurement of conformational changes with regarding to the reference structure, distinctive conformations may have same RMSD value. (C) Violin plot of RMSD values for the whole protein (core full length protein, not including NTD) and each domain. Here crystal structure was using as reference since the conformational changes difference between wild type and D170A was of interested. (D) The RMSD distribution of SH2 domain in the six replicas for D170A variant. (TIF)