The uses of synchrotron X-radiation in the crystallography of molecular biology

Crystal diffraction prediction and partiality estimation using Gaussian basis functions

The recent diversification of macromolecular crystallographic experiments including the use of pink beams, convergent electron diffraction and serial snapshot crystallography has shown the limitations of using the Laue equations for diffraction prediction. This article gives a computationally efficient way of calculating approximate crystal diffraction patterns given varying distributions of the incoming beam, crystal shapes and other potentially hidden parameters. This approach models each pixel of a diffraction pattern and improves data processing of integrated peak intensities by enabling the correction of partially recorded reflections. The fundamental idea is to express the distributions as weighted sums of Gaussian functions. The approach is demonstrated on serial femtosecond crystallography data sets, showing a significant decrease in the required number of patterns to refine a structure to a given error.

An RNA-centric historical narrative around the Protein Data Bank

Some of the amazing contributions brought to the scientific community by the Protein Data Bank (PDB) are described. The focus is on nucleic acid structures with a bias toward RNA. The evolution and key roles in science of the PDB and other structural databases for nucleic acids illustrate how small initial ideas can become huge and indispensable resources with the unflinching willingness of scientists to cooperate globally. The progress in the understanding of the molecular interactions driving RNA architectures followed the rapid increase in RNA structures in the PDB. That increase was consecutive to improvements in chemical synthesis and purification of RNA molecules, as well as in biophysical methods for structure determination and computer technology. The RNA modeling efforts from the early beginnings are also described together with their links to the state of structural knowledge and technological development. Structures of RNA and of its assemblies are physical objects, which, together with genomic data, allow us to integrate present-day biological functions and the historical evolution in all living species on earth.

The R-factor gap in macromolecular crystallography: an untapped potential for insights on accurate structures

In macromolecular crystallography, the agreement between observed and predicted structure factors (R_cryst and R_free) is seldom better than 20%. This is much larger than the estimate of experimental error (R_merge). The difference between R_cryst and R_merge is the R-factor gap. There is no such gap in small-molecule crystallography, for which calculated structure factors are generally considered more accurate than the experimental measurements. Perhaps the true noise level of macromolecular data is higher than expected? Or is the gap caused by inaccurate phases that trap refined models in local minima? By generating simulated diffraction patterns using the program MLFSOM, and including every conceivable source of experimental error, we show that neither is the case. Processing our simulated data yielded values that were indistinguishable from those of real data for all crystallographic statistics except the final R_cryst and R_free. These values decreased to 3.8% and 5.5% for simulated data, suggesting that the reason for high R-factors in macromolecular crystallography is neither experimental error nor phase bias, but rather an underlying inadequacy in the models used to explain our observations. The present inability to accurately represent the entire macromolecule with both its flexibility and its protein-solvent interface may be improved by synergies between small-angle X-ray scattering, computational chemistry and crystallography. The exciting implication of our finding is that macromolecular data contain substantial hidden and untapped potential to resolve ambiguities in the true nature of the nanoscale, a task that the second century of crystallography promises to fulfill.

Determination of macromolecular structures from anomalous diffraction of synchrotron radiation

Resonance between beams of x-ray waves and electronic transitions from bound atomic orbitals leads to a phenomenon known as anomalous scattering. This effect can be exploited in x-ray crystallographic studies on biological macromolecules by making diffraction measurements at selected wavelengths associated with a particular resonant transition. In this manner the problem of determining the three-dimensional structure of thousands of atoms is reduced to that of initially solving for a few anomalous scattering centers that can then be used as a reference for developing the entire structure. This method of multiwavelength anomalous diffraction has now been applied in a number of structure determinations. Optimal experiments require appropriate synchrotron instrumentation, careful experimental design, and sophisticated analytical procedures. There are rich opportunities for future applications.

A 6-GeV Storage Ring: An Advanced Photon Research Facility

The high brightness of synchrotron radiation produced by storage rings has enhanced research capability by factors of 10(6) to 10(8), from the ultraviolet to the x-ray region. There has been a steady growth in synchrotron radiation research of interest in physics, chemistry, biology, geology, and the other physical sciences and their associated technologies. A large number of university, government, and industrial research organizations are utilizing this new capability at existing facilities. In the process, new partnerships have been created among these communities that have enabled each to contribute its expertise and to obtain its needed capability. A 6-gigaelectron volt storage ring, designed for use with periodic magnetic insertion devices called wigglers and undulators, has been proposed; such a facility could provide further enhancements of 10(4) to 10(6) in capability and could double the synchrotron radiation research capacity in the United States. This enhanced capability and capacity will provide new opportunities for a broad range of scientific and technological interests.

Protein microcrystal diffraction and the effects of radiation damage with ultra-high-flux synchrotron radiation

By using ultra-high-flux synchrotron x-radiation from a wiggler source, good Laue diffraction data have been obtained from protein microcrystals of size 30 X 35 X 10 microns3, mounted wet in glass capillaries. At the flux level of 10(13)-10(14) photons per sec/mm2, the radiation damage is still low enough to allow a large survey of reciprocal space for a microcrystal and a complete survey for a normal-sized protein crystal. The development of sources for ultra-high-intensity synchrotron radiation is thus an important improvement in the technique for determination of structure through protein crystallography as well as in other cases where crystal size is often a limiting factor.

X-ray Laue Diffraction from Protein Crystals

In conventional x-ray diffraction experiments on single crystals, essentially monochromatic x-rays are used. If polychromatic x-rays derived from a synchrotron radiation spectrum are used, they generate a Laue diffraction pattern. Laue patterns from single crystals of macromolecules can be obtained in less-than 1 second, and significant radiation damage does not occur over the course of an exposure. Integrated intensities are obtained without rotation of the crystal, and individual structure factors may be extracted for most reflections. The Laue technique thus offers advantages for the recording of diffraction patterns from short-lived structural intermediates; that is, for time-resolved crystallography.