Table 1. The list of parameters used in the model and in calculation of derived measures.

Where not explicitly varied, the parameters are fixed at their default values.

Parameter	Symbol	Default value	Note
Chloroplast radius	rP	1.5 μm	From Ellis and Leech [18]
Chloroplast surface coverage	ϕplas/cell	50%	From Ellis and Leech [18]
Envelope-plasmalemma / envelope-tonoplast membrane separation	dsep	0.03 μm
Envelope and tonoplast membrane thickness	θmem	0.03 μm	The membrane thickness is exaggerated to improve numeric convergence. It does not affect the results except through excluded volume.
Vacuole drop	dV	$\frac{1}{2}{r}_P$	The depth by which the chloroplast ‘projects’ into the vacuole space (see Fig 1(a)).
Vacuole height	hV	1.5 × rP	The height (along the central axis) of the simulated part of the vacuole space.
RubisCO active site concentration	cR	4 mM	Known range is 2 mM-5 mM [25]
PEPC active site concentration	cP	variable
RubisCO carboxylation catalysis rate	vC	3.8 s-1	For T. aestivum from Cousins et al [38]
RubisCO oxygenation catalysis rate	vO	0.83 s-1
RubisCO Michaelis concentration for CO2	KC	9.7 μM
RubisCO Michaelis concentration for O2	KO	244 μM
PEPC carboxylation catalysis rate	vB	150 s-1	For Z. mays from Kai et al [39]
PEPC Michaelis concentration for HCO3-	KB	100 μM
CO2 pressure in the IAS	$p_{C{O}_2}$	250 μbar
O2 pressure in the IAS	$p_{O_2}$	0.21 bar
Henry constant for CO2 at 20°C	HC	38.5 mM/bar	From dissolved concentrations at 400 μbar and 210 μmbar taken from Carroll et al [40] and Murray and Riley [41].
Henry constant for O2 at 20°C	HO	1.36 mM/bar
pH in chloroplast stroma		8.0
pH in the cytoplasm		7.5
pH within the vacuole		5.5
CO2↔HCO3- conversion rate boost due to CA	ηCA	106	Saturating, see text.
Base rate for CO2+H2O→HCO3-+H+ reaction	$k_{C{O}_2}$	0.037 s-1	From Johnson [21].
Base rate for CO2+OH-→HCO3- reaction	$k_{OH-K_w}$	7.1 ⋅ 10−11 Ms-1
Base rate for HCO3-+H+→CO2+H2O reaction	kd	7.6 ⋅ 104 M-1s-1
Base rate for HCO3-→CO2+OH- reaction	$k_{HC{O}_3^{-}}$	1.8 ⋅ 10−4 s-1
Combined permeability of the cell wall and plasmalemma to O2 and CO2	σc	200 μm/s	Ranges in literature from 2 to 5 ⋅ 103μm/s [15, 42].
Permeability of the chloroplast envelope to O2 and CO2	σp	600 μm/s	Ranges in literature from 20 μm/s [43] to >3.6 cm/s [44].
Permeability of the tonoplast membrane to O2 and CO2	σv	2σp	Assumed to have similar properties to the membranes forming the envelope.
Permeability of the chloroplast envelope to HCO3-		1 nm/s	Essentially zero.
Permeability of the tonoplast membrane to HCO3-		2 nm/s
Diffusion constant for CO2 in water	DC,aq	1800 μm2/s	From Mazarei and Sandall [45]
Diffusion constant for O2 in water	DO,aq	1800 μm2/s	From Mazarei and Sandall [45]
Diffusion constant for HCO3- in water	DB,aq	1100 μm2/s	From Falkowski and Raven [46]
Cytoplasm viscosity relative to water	ηC	2	As in Tholen and Zhu [16].
Stroma viscosity relative to water	ηP	10
Vacuole interior viscosity relative to water	ηV	1
Chloroplast light-harvesting capacity	LHC	Varied	Either unlimited, or 40, or 80 mol m-3s-1.
Base photon cost of RuBP regeneration	φCalvin	8	From Zhu et al [29]
Base photorespiration photon cost	φphresp	9
Base cost of pyruvate-to-PEP conversion	φC4	4