Two common techniques for determining protein structure are (i) X-ray crystallography and (ii) nuclear magnetic resonance (NMR). (i) X-ray crystallography uses the interaction of X-rays with the electrons in a protein crystal to create an electron-density map of the molecule, which can be interpreted through an atomic model. The quality of the map depends on the resolution of the diffraction data, which is influenced by the order of the crystals. (ii) NMR uses the magnetic-spin properties of atomic nuclei within a molecule to obtain a list of distance constraints between atoms. In contrast to X-ray crystallography, NMR does not require protein crystals and can be used on proteins in concentrated solutions, but it has been limited to small proteins due to increasing complexity of NMR spectra with increasing size of molecules.

Experimentally determined protein structures may have uncertainty associated with them due to a variety of factors. One reason is that protein structures can be affected by variations in experimental conditions, such as temperature, pH, and the presence of other molecules. These variations can cause small changes in the protein's structure, which can be difficult to detect experimentally. Another reason for uncertainty in protein structures is that crystallized proteins represent only a snapshot of their true structures. Proteins are often flexible and dynamic molecules, and they can adopt different conformations depending on their environment and the specific tasks they are performing. This means that the structure of a protein determined using crystallography or NMR may not be representative of the protein's true structure under different conditions or in different environments.