Jim is deeply affected by Mr. Shimerda's suicide because he most identifies with his sense of pride. Mr. Shimerda was a successful man in his home country, moving his family for unselfish reasons. Jim appreciates his class and his need to present a positive appearance at all times. He also wonders how Unfortunately, living in such stark conditions and feeling so out of place.
Most importantly, Jim knows the unhappiness that Mr. Shimerda felt. WHile this unhappiness seemed to escape most of the family's and neighbors' notice, it did not escape Jim's. People speculate that perhaps Mr. Shimerda was murdered, though the evidence points otherwise. Jim devoutly disagrees. His comment below points to his understanding of Mr. Shimerda's suicide as it awakens his own latent feelings:
But Mr. Shimerda had not been rich and selfish: he had only been so unhappy that he could not live any longer.