Continuous Validation Across Macromolecular Structure Determination Process

Abstract

The overall quality of the experimentally determined structures contained in the PDB is exceptionally high, mainly due to the continuous improvement of model building and structural validation programs. Improving reproducibility on a large scale requires expanding the concept of validation in structural biology and all other disciplines to include a broader framework that encompasses the entire project. A successful approach to science requires diligent attention to detail and a focus on the future. An earnest commitment to data availability and reuse is essential for scientific progress, be that by human minds or artificial intelligence.

Fig.1

Multiple clones, expressions, purifications, crystallization drops, crystals and diffraction experiments for target IDP91778. Darker colors indicate pathway that resulted in structure determination. Screenshot from CSGID data management system.

Fig.2

The distribution of reported crystal temperatures during diffraction experiments. Over 127,000 deposits reported 100 K.

Fig.3

Different models of the metal binding site A201 in PDB 5XM5 deposit. Only the difference map is shown. (a) the binding site with Zn²⁺ (occupancy: 0.39), (b) the binding site with Zn²⁺ (occupancy: 1.0), (c) the binding site with Na⁺ (occupancy: 1.0).