Contrast: Module for Estimating the Contrast of Biomolecular Assemblies (v1.1.1 - 2017)

Project: KinA:SDA 2:2 complex in 200mM NaCl, 50mM Tris, 150mM imidazole

Analysis of the dependence of I(0) upon f_D₂O

Approximate X-intercept = 0.504 (Determined from 2^nd order polynomial fit to I(0)/c vs. f_D₂O)

Linear fit to √I(0)/c vs. f_D₂O (sign of √I(0)/c for f_D₂O > approximate X-intercept adjusted)

I(0) analysis
Parameter Value ESD
χ² 61.59 -
Slope -0.428 0.003
Y-intercept 0.216 0.002
X-intercept 0.505 0.003

*I(0) analysis*
Parameter	Value	ESD
χ²	61.59	-
Slope	-0.428	0.003
Y-intercept	0.216	0.002
X-intercept	0.505	0.003

Contrast calculation parameters

In addition to water the solvent contains 3 other substance(s)

Molecule(NaCl), Conc. = 0.200 mol/L, Volume of each formula unit to be calculated
Molecule(H_11.0C_4.0NO_3.0), Conc. = 0.050 mol/L, Volume of each formula unit to be calculated
Molecule(H_4.0C_3.0N_2.0), Conc. = 0.150 mol/L, Volume of each formula unit to be calculated

Subunit (1) - possesses 1 component(s), with a deuteration level of 0% and 95% of the total exchangeable protons accessible by the solvent

Protein(228 residues - H_1823.0C_1135.0N_297.0O_343.0S_7.0), 2 formula unit(s), Volume of each formula unit to be calculated

Subunit (2) - possesses 1 components(s), with a deuteration level of 85% and 100% of the total exchangeable protons accessible by the solvent

Protein(48 residues - H_401.0C_244.0N_68.0O_77.0S_2.0), 2 formula unit(s), Volume of each formula unit to be calculated

Contrast calculation results

Solvent and particle information in H₂O
Volume
(Å³) Σb_X
(10^-13cm) Σb_N
(10^-13cm) ρ_X
(10¹⁰cm^-2) ρ_N
(10¹⁰cm^-2) Mass
(kDa)
Solvent
54.59 30.0 28.18 -1.68 9.403 -0.560 0.018
0.20 29.3 78.90 13.21 26.938 4.509 0.058
0.05 152.3 185.98 12.20 12.212 0.801 0.121
0.15 74.9 101.45 23.69 13.544 3.163 0.068
Total - 1578.48 -84.84 9.506 -0.511 -
Subunit (1) - Number of hydrogen atoms = 3646.0, Number of exchangeable hydrogen atoms = 762.0
2.00 62695.1 76467.63 11027.29 12.197 1.759 50.685
Total 62695.1 76467.63 11027.29 12.197 1.759 50.685
Subunit (2) - Number of hydrogen atoms = 802.0, Number of exchangeable hydrogen atoms = 190.0
2.00 13711.7 16845.65 7837.30 12.286 5.716 11.690
Total 13711.7 16845.65 7837.30 12.286 5.716 11.690

*Solvent and particle information in H₂O*
	Volume (Å³)	Σb_X (10^-13cm)	Σb_N (10^-13cm)	ρ_X (10¹⁰cm^-2)	ρ_N (10¹⁰cm^-2)	Mass (kDa)
Solvent
54.59	30.0	28.18	-1.68	9.403	-0.560	0.018
0.20	29.3	78.90	13.21	26.938	4.509	0.058
0.05	152.3	185.98	12.20	12.212	0.801	0.121
0.15	74.9	101.45	23.69	13.544	3.163	0.068
Total	-	1578.48	-84.84	9.506	-0.511	-
Subunit (1) - Number of hydrogen atoms = 3646.0, Number of exchangeable hydrogen atoms = 762.0
2.00	62695.1	76467.63	11027.29	12.197	1.759	50.685
Total	62695.1	76467.63	11027.29	12.197	1.759	50.685
Subunit (2) - Number of hydrogen atoms = 802.0, Number of exchangeable hydrogen atoms = 190.0
2.00	13711.7	16845.65	7837.30	12.286	5.716	11.690
Total	13711.7	16845.65	7837.30	12.286	5.716	11.690

The neutron scattering length density (10¹⁰cm^-2) at any D₂O fraction is:

ρ₁ = 1.759 + 4.790f_D,1 + 1.265f_AccessH,1f_D₂O = 1.759 + 1.202f_D₂O
ρ₂ = 1.766 + 4.647f_D,2 + 1.443f_AccessH,2f_D₂O = 5.716 + 1.443f_D₂O
ρ_s = -0.511 + 6.845f_D₂O

The neutron contrast (10¹⁰cm^-2) at any D₂O fraction is:

Δρ₁ = 2.270 + 4.790f_D,1 - 5.580f_AccessH,1f_D₂O = 2.270 - 5.643f_D₂O
Δρ₂ = 2.277 + 4.647f_D,2 - 5.403f_AccessH,2f_D₂O = 6.227 - 5.403f_D₂O
Δρ = 2.271 + 3.930f_D,1 + 0.834f_D,2 + 1.038f_AccessH,1f_D₂O + 0.259f_AccessH,2f_D₂O - 6.845f_D₂O = 2.980 - 5.600f_D₂O

*Tabulated scattering length densities and contrasts*
	ρ (10¹⁰cm^-2)			Δρ (10¹⁰cm^-2)
	1	2	Solvent	1	2	Total
X-RAY	12.197	12.286	9.506	2.691	2.780	2.707
NEUTRON
0.0	1.759	5.716	-0.511	2.270	6.227	2.980
0.1	1.879	5.860	0.174	1.706	5.686	2.420
0.2	1.999	6.004	0.858	1.141	5.146	1.860
0.3	2.120	6.149	1.543	0.577	4.606	1.300
0.4	2.240	6.293	2.227	0.013	4.066	0.740
0.5	2.360	6.437	2.912	-0.552	3.525	0.180
0.6	2.480	6.581	3.596	-1.116	2.985	-0.380
0.7	2.600	6.726	4.281	-1.680	2.445	-0.940
0.8	2.721	6.870	4.965	-2.245	1.905	-1.500
0.9	2.841	7.014	5.650	-2.809	1.364	-2.060
1.0	2.961	7.159	6.334	-3.373	0.824	-2.620
Calculated match-point (f_D₂O)				0.402	1.153	0.532
Experimental match-point (f_D₂O)				-	-	0.505(3)

Other related quantities

The density (in g.cm^-3 @ 20°C) of the solvent at any D₂O fraction is:

Density = 1.011 + 0.105f_D₂O

The molecular mass (kDa) at any D₂O fraction is:

Mass₁ = 50.685 + 2.901f_D,1 + 0.728f_AccessH,1f_D₂O = 50.685 + 0.692f_D₂O
Mass₂ = 11.167 + 0.616f_D,2 + 0.191f_AccessH,2f_D₂O = 11.690 + 0.191f_D₂O

The partial specific volume (cm³g^-1, fully proteated) is:

ν₁ = 0.745
ν₂ = 0.739
ν = 0.744

The X-ray scattering length per unit mass (10¹⁰cm.g^-1) is:

ρ_M,1 = 9.086
ρ_M,2 = 9.085
ρ_M = 9.085