X-ray diffraction experiment--the last experiment in the structure elucidation process

Abstract

Recent years have brought not only an avalanche of new macromolecular structures, but also significant advances in the protein structure determination methodology only now making its way into structure-based drug discovery. In this chapter, we review recent methodology developments in X-ray diffraction experiments that led to fast and very accurate elucidation of three-dimensional structures of macromolecules. We will discuss the role of data collection as the last experiment performed in the crystal structure determination process. A statistical analysis of diffraction experiments that are reported in the Protein Data Bank (PDB) is also presented.

Figure 1

Fraction of deposits determined with the use of CCD detectors by data collection year. The blue bars represent the fraction of PDB deposits solved using synchrotron radiation, while the red bars represent the fraction of deposits solved using home systems.

Figure 2

The resolution of structures solved by MR as a function of the sequence identity of the most similar homolog in the PDB at the time of deposition. The figure shows only cases where the sequence identity of the most similar structure smaller or equal to 90%. Red circles represent structures with one macromolecular chain in the asymmetric unit.

Figure 3

Ratio of total amino acid residues to number of ordered Se-Met residues, plotted as a function of the structure resolution. Structures solved by SAD are shown as red circles and those solved by MAD as green circles.

Figure 4

PDB deposits grouped by the wavelength used during the diffraction experiment. Only deposits obtained with synchrotron radiation are shown.

Figure 5

Distribution of mean I/σI vs. I/σI for the highest resolution shell for structures reported in the PDB.

Figure 6

Distribution of R_merge vs. R_merge for the highest resolution shell for structures reported in the PDB.

Figure 7

R factor vs. resolution for four PSI centers. Each center is represented by different color of data points and trend lines.