Recent national calls to transform undergraduate science education have centered on engaging students in scientific practices as a means to help them develop deeper insights into science. The three-dimensional framework for science education encapsulates the goals of these national calls by recommending that instructors integrate scientific practices, crosscutting concepts, and disciplinary core ideas throughout their courses. Prior research has found that introductory undergraduate biology exams contain few three-dimensional items suggesting that instructors likely face barriers in meeting the goals of national calls. To better understand these putative challenges, we explored factors potentially associated with three-dimensional alignment. Our generalized linear mixed model indicated that instructors who used three-dimensional items on their exams were more likely to use Bloom's Taxonomy when designing their exams and were more likely to write these items using a constructed-response format. We also found that professional development opportunities did not necessarily change the likelihood an instructor would employ three-dimensional items. We previously identified that few items in our sample fully aligned to scientific practices, making scientific practices the limiting dimension for three-dimensional alignment. Our subsequent analysis here revealed that most biology instructors had exam items that were at least partially aligned to scientific practices. Based on our results, we highlight the significant time and resources that instructors likely need to write and grade constructed-response assessments, suggest that instructors build on items that are mostly aligned to scientific practices to increase their three-dimensional alignment, and propose ways that professional development programs and communities might further support instructors in meeting national calls.