Looking Past the Pictures: Evaluating X-Ray Crystal Structure Papers

©2008 Elsevier Inc. All rights reserved. 7 Introduction There is an ever-increasing reliance on X-ray crystallography for understanding biomolecular function. This method produces atomic-resolution images of protein and nucleic acids that typically capture one or more physiologically relevant states of the molecule under investigation. Such structural information can be used to understand a wide variety of key biophysical processes, from the chemistry of enzyme catalysis and small-molecule inhibition to processes of conformational change and macromolecular assembly. By January 2007, over 40,000 structures had been solved and deposited in the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (Berman et al., 2000). These structures have been accompanied by an explosion of papers that describe only a fraction of the tremendous variety of molecular architectures that exist in nature. Given the impact of structural data on modern molecular biological inquiry, it is important to recognize some of the limitations inherent in the method. Similarly, because “structures” are actually models that account for experimentally derived diffraction data, it is essential to understand the statistics and numbers listed in structure papers to evaluate model accuracy and veracity. This review describes some of the important features of these papers and explains the meaning behind the numerical descriptors one is likely to encounter. For more thorough treatments of topics such as crystal growth or data acquisition and analysis, the reader is invited to see Drenth (2006), McPherson (1999), and Rhodes (2006). Overview of the Method To determine a crystal structure, an experimentalist first needs high-quality crystals of the protein or nucleic acid target of interest. By manipulating chemical conditions that influence solubility, many proteins and nucleic acids can be coaxed from their solution state into a crystalline array. Although crystal formation may at first seem an unnatural process that might constrain or alter the structure of a target macromolecule, numerous comparisons between crystal structures and data obtained from other spectroscopic methods (e.g., nuclear magnetic resonance; NMR) have suggested this is not the case. Indeed, crystallization is a relatively gentle process that actually captures one or more preexisting conformational states of the molecule that are already present in solution, as opposed to forcibly “wedging” the target into a rigid lattice. Moreover, protein and nucleic acid crystals are highly solvated (typically containing 40%–60% water), and possess interior macromolecule concentrations approaching those found inside cells. Finally, many enzymes retain catalytic activity in the crystalline state, permitting high-resolution imaging of their chemical reactions. Taken together, these properties mean that physiologically relevant insights into function can be derived from crystal structures. If the molecular packing of a crystal is suitably uniform and ordered, defined diffraction patterns can be obtained from the sample upon its exposure to an intense beam of collimated X-rays (Figure 1A). X-rays are electromagnetic waves, and possess all the physical characteristics that describe a wave, including amplitude, phase, and wavelength (Figure 1B, upper). Being Looking Past the Pictures: Evaluating X-Ray Crystal Structure Papers