Abstract
Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
Highlights
Macromolecules are essential for biological processes within organisms, engendering the need to understand their behavior to explain the fundamentals of life
Two major methods to obtain macromolecular structures are diffraction and electron cryomicroscopy (Fig. 1), both of which are handled by Phenix
The number of structures determined by neutron crystallography (0.1% of the models deposited in the Protein Data Bank (PDB)) is small compared with the number of X-ray structures (89%)
Summary
Macromolecules are essential for biological processes within organisms, engendering the need to understand their behavior to explain the fundamentals of life. Two major methods to obtain macromolecular structures are diffraction (usually using X-rays, and neutrons or electrons) and electron cryomicroscopy (cryo-EM1) (Fig. 1), both of which are handled by Phenix. X-ray diffraction X-ray diffraction relies on the interaction of X-rays with the electron cloud of atoms in a crystal. The neutron scattering length can be positive or negative (it is always positive for X-rays). To avoid negative scattering from H atoms, hydrogen can be partially or fully exchanged with deuterium by soaking the crystal in deuterated buffer solutions or by performing protein expression in fully deuterated reagents, respectively. Neutron diffraction is not used to solve the structure of a macromolecule de novo as it requires considerable effort to prepare deuterated crystals suitable for the experiment. Neutron diffraction provides complementary information because it enables the location of H or D atoms
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callMore From: Acta crystallographica. Section D, Structural biology
Disclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
