Fig. 7.

Increasing the dead time, $t_d$, helps approximately correct for missed transitions. We combine 10 $N=1$ in vitro traces and use the combined traces to determine rates and N (whose theoretical value should be $N=10$). We generated 1,000 of such traces (with 200 bootstrap iterations). The distribution over N is shown for increasing values of $t_d$. Dendra2 has a dwell time in the bright state, which is on average approximately as long as the time resolution of experiment (50 ms). Thus, when $t_d$ is zero, approximately half the transitions to the bright state are missed. As $t_d$ increases, our estimate for N improves. Fig. 4 shows that PA-FPs with kinetics slower than the integration time should improve the estimate for N.