Table 1. Model parameter values.

Symbol	Description	FC (day)	FC (night)	FR
	Minimal Toc1 transcription rate (nM/min)	0.0017	0.0016	0.0065
	CCA1-dependent Toc1 transcription rate (nM/min)	0.93	0.29	0.67
	CCA1 level at Toc1 repression threshold (nM)	1.47	0.00	1.04
	Cooperativity of CCA1	2	2	2
	mTOC1 half-life (min)	13.8	22.0	5.08
	mTOC1 degradation saturation threshold (nM)	8.85	18.3	1.25
	TOC1 translation rate (1/min)	0.013	0.023	0.016
	TOC1 half-life (min)	29.9	29.0	3.58
	TOC1 degradation saturation threshold (nM)	3.85	9.78	0.76
	Minimal Cca1 transcription rate (nM/min)	0.0075	0.017	0.052
	TOC1-dependent Cca1 transcription rate (nM/min)	0.12	0.047	0.060
	TOC1 level at Cca1 activation threshold (nM)	100.4	1.49	44.1
	Cooperativity of CCA1	2	2	2
	mCCA1 half-life (min)	13.3	52.2	0.82
	mCCA1 degradation saturation threshold (nM)	0.56	3.76	0.063
	CCA1 translation rate (1/min)	0.056	0.046	0.075
	CCA1 half-life (min)	55.5	92.3	54.7
	CCA1 degradation saturation threshold (nM)	32.4	36.0	46.0

Parameter values result from adjusting model (2) to experimental data (see Methods) with (i) all parameter values varying between day and night (fully coupled model, FC, Fig. 2(A)) and (ii) all parameter values constant (free-running model, FR, Fig. 2(B)).