Supporting Information
Sontz et al. 10.1073/pnas.1120063109
Table S1. Binding density ratios for AFM samples
Sample
BDR*,
†
Long strands Proteins Short strands Proteins Error (%)
‡
Prot/kbp
0.6
μ
M XPD
0.94
307
216
360
142
5.3
0.19
0.6
μ
M XPD (C
∶
A)
1.54
354
304
323
95
5
0.20
0.3
μ
M XPD
1.08
304
123
502
99
6.7
0.11
0.3
μ
M XPD (C
∶
A)
1.38
376
271
354
97
5.2
0.18
L325V 0.6
μ
M
1.05
221
149
251
85
6.5
0.18
L325V 0.6
μ
M(C
∶
A)
1.14
311
236
415
145
5
0.19
XPD/EndoIII
1
∶
1
1.02
221
127
257
76
7
0.15
XPD/EndoIII
1
∶
1
(C
∶
A) 1.75
253
150
370
66
7.6
0.13
XPD/Y82A
1
∶
1
1.11
468
183
665
123
6
0.10
XPD/Y82A 1:1 (C
∶
A)
0.98
496
258
538
150
5
0.14
EndoIII/L325V
1
∶
1
0.94
327
263
412
186
4.7
0.22
EndoIII/L325V
1
∶
1
1.02
361
217
553
171
5.1
0.16
XPD/L325V
1
∶
1
0.90
309
174
408
134
5.7
0.16
XPD/L325V
1
∶
1
(C
∶
A)
0.88
564
329
653
227
4.2
0.16
*Binding Density Ratio (BDR) is reported as [number of proteins bound on long strands (3.8 kbp) /number of long strands]
divided by the [number of proteins on short strands (1.9 kbp)/number of short strands] normalized for length. (C
∶
A)
represents samples with long mismatched strands.
†
These data represent three individual samples with 10
–
20 images per sample. L325V is a mutant of wild type XPD, and Y82A
is a mutant of wild type EndoIII.
‡
Error is reported as the (total number of proteins divided by the square root of the total number of proteins counted) times
100 for each type of sample.
Sontz et al.
www.pnas.org/cgi/doi/10.1073/pnas.1120063109
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