The results of NMR analysis are an ensemble of alternative models, in contrast to the unique model obtained by crystallography. Structures obtained by theoretical modeling tend to be less accurate than those obtained by experimental methods. One kind of modeling, called homology modeling, involves fitting a known sequence to the experimentally determined 3D structure of a sequence-similar molecule. There are several experimental hurdles which must be crossed before the 3D structure of a macromolecule can be determined by X-ray diffraction from crystals. Countless attempts to determine molecular structures have failed at this stage.
Protein crystallization is as much an art as a science.
Many important molecules are absent from the PDB because attempts to produce suitable crystals failed. Once a crystal is obtained, a diffraction pattern is produced by X-irradiation. This pattern consists of thousands of spots which are the raw data. The position and intensity of each spot is relatively easily determined, but the phases of the waves which formed each spot must also be determined in order to produce an electron density map. Often this has been accomplished by irradiating two or more derivatives of the same crystal which differ only in the presence of heavy metal ions.