Appendix 1—figure 1. A cutoff value of 8.0 Å produces more accurate values for the number of unwrapped DNA base pairs as determined from visual inspection of representative configurations, related to Figure 2 of the main text.

See text section ‘Number of unwrapped DNA base pairs’ for additional discussions. A typical nucleosome structure with most of the outer layer DNA unwrapped was used to examine the impact of different cutoff values. The histone core is colored in gold, with histone tails in white, the wrapped DNA in blue, and the unwrapped DNA in red. The discrepancy among various cutoff values is evident in the highlight regions enclosed by dotted circles. As shown in the zoom-ins in the middle panel, a cutoff of 10 Å results in three additional base pairs of DNA detected as wrapped in I (highlighted in orange square). However, these extra base pairs not detected with a cutoff of 8 Å are visibly detached from histone proteins. Similarly, 9 Å and 10 Å cutoff values result in five extra base pairs of DNA detected as wrapped in II (highlighted in orange squares in the bottom panel).