Supercell refinement: a cautionary tale.

Area of Science:

• Crystallography
• Materials Science
• Structural Biology

Background:

• Crystals with supercells can be viewed as large unit cells or higher-dimensional superspaces with commensurate modulations.
• In modulated structures, an average structure model is often used, with modulation functions defining atomic positions.

Purpose of the Study:

• To investigate the feasibility of solving incommensurately modulated protein crystals using a supercell approximation.
• To test refinement methods by comparing solutions against a known model structure.

Main Methods:

• A model protein structure and simulated diffraction data were utilized.
• An average structure was solved using main reflections (subset of subcell reflections).
• The average structure was expanded to a supercell and refined using all reflections.

Main Results:

• Refinement of the supercell approximation did not yield the expected structure, despite excellent statistical indicators.
• The refinement process converged on an alternate 3D daughter supercell space group, not the intended one.
• The identified superspace group presented multiple possible 3D daughter space groups.

Conclusions:

• Supercell approximations in crystallography may lead to the selection of unintended daughter space groups during refinement.
• These findings necessitate careful consideration when analyzing incommensurately modulated structures, such as profilin-actin crystals.
• Future work will apply these lessons to a real incommensurately modulated profilin-actin crystal.