First Lanthanide Complex for De Novo Phasing in Native Protein Crystallography at 1 Å Radiation

Phasing agents enabling de novo protein structure determination at ca. 1 A, the wavelength corresponding to the maximum intensity of the synchrotron facilities applied in biomacromolecular crystallography, have been long sought-after. The first phasing agent designed for solving native protein structures at 0.97934 A is described herein. The agent consists of a neutral ytterbium(III)-caged complex that exhibits higher anomalous signals at shorter wavelengths when compared to the best, currently applied lanthanide-based phasing agents, all of them based on gadolinium or terbium. As a proof of principle, the complex allows determining the 3D structure of a 36 kDa protein without setting the incident beam wavelength at the metal absorption edge, the strategy followed to date to gain the strongest anomalous signal even at the expense of crystallographic resolution. The agent becomes nondisruptive to the diffraction quality of the marked crystals and allows determining accurate phases, both leading to high-quality electrondensity maps that enable the full tracing of the protein structure only with one agent unit bound to the protein. The high phasing power, efficient binding to the protein, low metal-macromolecule ratio, and easy handling support the developed Yb(III) complex as the best phasing agent for X-ray crystallography of a complex biomacromolecule without using modified analogues.

Automated summary

The study introduces a ytterbium(III) complex as a phasing agent for de novo protein structure determination at approximately 1 A, offering high phasing power and high-quality electron density maps while maintaining crystallographic resolution. This agent presents a new possibility for X-ray crystallography of complex biomacromolecules.