Crystal Meanings of Agate. Keywords: Protection, Strength, Harmony. Agate's most noticeable properties overall are balancing yin/yang energy, courage, protection, healing, and calming. Historically it was placed in water for cooking or drinking to dispel sickness. Agate is a cryptocrystalline variety of silica, chiefly chalcedony, characterized by its fineness of grain and brightness of color.