Which method is commonly used to analyze protein structure?

X-ray crystallography is a widely utilized method for analyzing protein structure because it allows researchers to determine the three-dimensional arrangement of atoms within a protein at atomic resolution. This technique involves crystallizing the protein and then measuring the diffraction of X-rays that pass through the crystal. By analyzing the resulting diffraction pattern, scientists can infer the electron density map and, subsequently, the precise positions of atoms in the protein structure.

This method is particularly powerful for its ability to provide detailed structural information, which is essential for understanding the function of proteins as well as for drug design and development. The high-resolution images generated can reveal critical insights into the protein's active sites and interactions with other molecules, which are key factors in biochemical processes.

While other methods mentioned, such as nuclear magnetic resonance and mass spectrometry, also offer valuable insights into protein characteristics, X-ray crystallography is considered the gold standard for determining the static structure of proteins with high accuracy. Electrophoresis is used primarily for separating proteins based on size or charge but does not provide structural details per se. Therefore, in the context of analyzing protein structure, X-ray crystallography stands out as the method of choice.