To explore dense packings of soft colloids, scattering experiments are ideal to access the structure factor. However, for soft microgels determination of the structure factor is difficult because of the low contrast of the polymer network and potential microgel interpenetration and deformation that change the form factor contribution. Here, we employ small-angle X-ray scattering (SAXS) to study soft, thermoresponsive microgels with poly-N-isopropylacrylamide (PNIPAM) shells and gold nanoparticle cores. The scattering of the gold cores dominates the scattering patterns and allows precise determination of the microgel volume fraction over a broad range of concentrations. At high volume fractions we find distinct patterns with sharp Bragg peaks allowing extraction of the structure factor and characterization of the phases combined with UV-Vis spectroscopy. The unique scattering contrast of our core-shell microgels combined with SAXS opens up new ways to investigate dense packings of soft microgels including in situ studies of phase transitions.