Appendix 1—table 4.

Kinetic model determination for Mbo holo+RbpA+CarD on the Cy3-AP3 promoter.

DOI: http://dx.doi.org/10.7554/eLife.22520.027

	Mbo holo+RbpA+CarD**
Model*	1-step	2-step	3-step	4-step
k1 (M−1s−1)	(2.7 ± 0.1) x 107	(1.2 ± 0.2) x 108	(1.1 ± 0.2) x 108	(5.4 ± 0.3) x 107
k-1 (s−1)	(6.1 ± 1.5) x 10−3	27 ± 5	20 ± 5	2.0 ± 0.4
K1 (M−1)	(4.4 ± 1.1) x 109	(4.4 ± 1.1) x 106	(5.5 ± 1.7) x 106	(2.7 ± 0.6) x 107
k2 (s−1)		9.6 ± 0.4	9.7 ± 0.5	3.9 ± 0.5
k-2 (s−1)		1.1 × 10−7	0.031 ± 0.011	0.11 ± 0.43
K2		8.7 × 107	310 ± 11	35 ± 140
k3 (s−1)			0.13 ± 0.03	11 ± 34
k-3 (s−1)			(1.3 ± 8.2) x 10−3	9.0 ± 30
K3			100 ± 63	1.2 ± 5.6
k4 (s−1)				0.16 ± 0.42
k-4 (s−1)				(2.9 ± 3800) x 106
K4				7.6 ± 40
χ2/DOF	1.32367	1.09473	1.05035	1.0458
kd†	6.1 × 10−3	1.1 × 10−7	2.5 × 10−4	4.3 × 10−7
t1/2 (min)	1.9	1.1 × 105	47	2.7 × 104
t1/2exp (min)‡	~30
a	0.59	0.63	0.28	0.91
b	1.7	0.63	0.28	0.95
c		1.6	1.2	4.2
d			1.3	5.7 × 10−6
e				1.9
bkg	0.34	0.28	0.63	1.1 × 10−6

*Appendix 1—figure 1.

**The errors listed are the standard errors from the global fit as reported by Kintek Global Kinetic Explorer (Johnson et al., 2009a).

^†For the 1-step, 2-step, and 3-step models, the value for k_d, the dissociation rate for RPo, was calculated using equation (17) of Tsodikov and Record (1999):.

$${\displaystyle \frac{1}{k_{\text{d}}}=\frac{1}{k_{-3}}+\frac{1+{\text{K}}_3}{k_{-2}}+\frac{{\text{K}}_2+{\text{K}}_2{\text{K}}_3}{k_{-1}}+\frac{1}{k_{-1}}}$$ (2)

.

For the 1-step model, K₂ = K₃ = 0, k_-2 = k_-3 = ∞; for the 2-step model, K₃ = 0, k_-3 = ∞. For the 4-step model, dissociation was simulated and the result was fit to a single exponential decay to derive k_d. The value for t_1/2 was calculated as t_1/2 = ln(2)/k_d.

c^‡The experimental half-life (t_1/2^exp) was determined from promoter lifetime experiments (Figure 2C).