The modified atomic scattering amplitudes (MASAs) of mixed Ga1-xInxAs, GaAs1-xNx, and InAs1-xNx are calculated using the density functional theory approach and the results are compared with those of the binary counterparts. The MASAs of N, Ga, As, and In for various scattering vectors in various chemical environments and in the zinc-blende structure are compared with the frequently used Doyle and Turner values. Deviation from the Doyle and Turner results is found for small scattering vectors (s≪0.3 Å-1) and for these scattering vectors the MASAs are found to be sensitive to the orientation of the scattering vector and on the chemical environment. The chemical environment sensitive MASAs are used within zero pressure classical Metropolis Monte Carlo, finite temperature calculations to investigate the effect of well size on the electron 002 and 220 structure factors (SFs). The implications of the use of the 002 (200) spot for the quantification of nanostructured Ga1-xInxAs systems are examined while the 220 SF across the well is evaluated and is found to be very sensitive to the in-plane static displacements.