Advances in nano-computed X-ray tomography (nCT), nano X-ray fluorescence spectrometry (nXRF), and high-performance computing have enabled the first direct comparison between observations of three-dimensional nanoscale microstructure evolution during cement hydration and computer simulations of the same microstructure, using HydratiCA. nCT observations of a collection of triclinic tricalcium silicate (Ca3SiO5) particles reacting in a calcium hydroxide solution are reported and compared to simulations that duplicate, as nearly as possible, the thermal and chemical conditions of those experiments. Particular points of comparison are the time dependence of the solid phase volume fractions, spatial distributions, and morphologies. Comparisons made at 7 hours of reaction indicate that the simulated and observed volumes of Ca3SiO5 consumed by hydration agree to within the measurement uncertainty. The location of simulated hydration product is qualitatively consistent with the observations, but the outer envelope of hydration product observed by nCT encloses more than twice the volume of hydration product in the simulations at the same time. Simultaneous nXRF measurements of the same observation volume imply calcium and silicon concentrations within the observed hydration product envelope that are consistent with Ca(OH)(2) embedded in a sparse network of calcium silicate hydrate (C-S-H) that contains about 70% occluded porosity in addition to the amount usually accounted as gel porosity. An anomalously large volume of Ca(OH)(2) near the particles is observed both in the experiments and in the simulations, and can be explained as originating from the hydration of additional particles outside the field of view. Possible origins of the unusually large amount of observed occluded porosity are discussed.