Recent advancements in computer graphics and hardware have driven the resurgence of virtual reality (VR). Past literature has reported the use of VR in education, especially for teaching spatially complex concepts. However, there are limited data available on the precise role of VR game design elements. In this study, we introduce a new VR game, "Crystal Vision," which is designed to teach basic crystallographic concepts to undergraduate students. By systematically testing this VR game on a set of 84 students, we find that a VR-based intervention resulted in a 9% increase in their quiz scores (from 7.45 ± 0.16 to 8.12 ± 0.16) and a simultaneous 19% decrease in their quiz completion times (from 7.39 ± 0.24 to 5.98 ± 0.26 min). Finally, we find that a majority of students who felt comfortable while moving through the game indicated a higher level of agreement on most of the survey questions, indicating that user comfort within a VR game plays a significant role in influencing student learning outcomes.