Proteins are much larger than these molecules and their structure determination was commensurately more difficult. Whereas vitamin B12 has fewer than 200 atoms, even the smallest proteins have well over 1000 atoms and the largest proteins may have between 10000 and 100000 atoms. The first solved protein crystal structure was of Sperm Whale myoglobin, as determined by Max Perutz and Sir John Cowdery Kendrew in 1958, for which they were awarded the Nobel Prize in Chemistry in 1962. In the life sciences, X-ray crystallography is used widely by pharmaceutical companies, who use crystallography to determine specifically how drug lead compounds interact with their protein targets, and by academic researchers who can use crystallography as a powerful tool to understand how a particular macromolecule accomplishes its various functions. Biological X-ray crystallography is, to date, the most prolific discipline within the area of structural biology; out of the ~42000 protein structures solved, X-ray crystallography is responsible for ~36000. NMR spectroscopy has contributed almost 6000 and electron microscopy just over 140. Other biophysical methods, such as IR spectroscopy and powder diffraction make up the remaining structures, according to the Protein Data Bank (PDB).

The number of protein structures that have been determined is growing rapidly and current high-throughput methods have allowed the development of the new field of structural genomics. These projects aim to determine over 10,000 protein structures over the next few years, giving a vast new resource to the structural biology field. However, a major hindrance to these efforts is the difficulty in crystallizing membrane proteins, which make up a large proportion of proteins of pharmacological importance, such as ion channels and receptors.