Determining the structure of a protein has been a decades-long open question. A protein's three-dimensional structure often poses nontrivial computation costs, when classical simulation algorithms are utilized. Advances in the transformer neural network architecture achieve significant improvements for this problem, by learning from a large dataset of sequence information and corresponding protein structures. Yet, such methods often only focus on sequence information; other available prior knowledge, such as protein crystallography and partial structure of amino acids, could be potentially utilized. To the best of our knowledge, we propose the first transformer-based model that directly utilizes protein crystallography and partial structure information to predict the electron density maps of proteins. Via two new datasets of peptide fragments (2-residue and 15-residue), we demonstrate our method, dubbed CrysFormer, can achieve accurate predictions, based on a much smaller dataset size and with reduced computation costs.