Figure 2.

Distances between crossed-linked atoms in XL-MS experiments using BS³ or DSS and proteins with known experimental structures. The data come from the compilation of Kahraman et al.³⁰ Distributions (black) and cumulative distributions (red) are shown with 1-Å bins. The gray lines show the conventional cutoff distances of 11.4 Å for N_ζ and 24.4 Å for C_α. The total number of crosslinks included in the data is 502. (A) Experimental N_ζ–N_ζ distances. Note that the central tendency of the N_ζ–N_ζ distances is considerably larger than the 11.4-Å span of the fully extended BS³ linker, and that the distribution has a heavy tail at larger distances. (B) Experimental C_α–C_α distances. The C_α–C_α distance distribution peaks at distances considerably lower than the maximum theoretical C_α–C_α distance (24 Å, see Fig. 1).