There has been a growing request from the X-ray astronomy community for a quantitative estimate of systematic uncertainties originating from the atomic data used in plasma codes. Though there have been several studies looking into atomic data uncertainties using theoretical calculations, in general, there is no commonly accepted solution for this task. We present a new approach for estimating uncertainties in the line emissivities for the current models of collisional plasma, mainly based upon a dedicated analysis of observed high resolution spectra of stellar coronae and galaxy clusters. We find that the systematic uncertainties of the observed lines consistently show an anticorrelation with the model line fluxes, after properly accounting for the additional uncertainties from the ion concentration calculation. The strong lines in the spectra are in general better reproduced, indicating that the atomic data and modeling of the main transitions are more accurate than those for the minor ones. This underlying anticorrelation is found to be roughly independent of source properties, line positions, ion species, and the line formation processes. We further applied our method to the simulated XRISM and Athena observations of collisional plasma sources and discuss the impact of uncertainties on the interpretation of these spectra. The typical uncertainties are 1-2% on temperature and 3-20% on abundances of O, Ne, Fe, Mg, and Ni.