Global quality assessment

Assessing the quality of macromolecular models is critical to ensure the reliability and interpretability of any structural data you plan to use in your research. This section will introduce you to global quality assessment, covering the common metrics used to evaluate models obtained through various methods, including X-ray crystallography (X-ray), cryo-electron microscopy (cryo-EM), and nuclear magnetic resonance (NMR) spectroscopy.

We will also explore how these global assessments contribute to the overall confidence in using a particular structural model and, importantly, where to find this information quickly and easily.

Before going into the details of macromolecular models, it’s helpful to think of a 3D structure as a hypothesis. This hypothesis proposes a specific arrangement of atoms in space. To determine how plausible and reliable this hypothesis is, we need to validate it using various forms of evidence.

• Experimental evidence: Does the model accurately reflect the raw experimental data collected? For example, does it fit the diffraction patterns in X-ray crystallography or the images in cryo-EM?
• Prior knowledge: Does the model adhere to fundamental principles of protein chemistry, known structural features (e.g. standard bond lengths and angles), and the basic laws of physics?

A structural model makes specific claims about atomic positions, and its reliability depends on how well these claims are supported by the experimental evidence and chemical/physical plausibility.

What makes a “good model” is its ability to satisfy these criteria, being physically plausible, chemically sensible, and experimentally sound relative to the data from which it was derived. This validation process helps you understand how trustworthy the model is for answering your specific biological questions.

By the end of this section you will be able to:

• Identify the most important global quality metrics for structures determined by X-ray, cryo-EM and NMR.
• Explain what these key metrics generally indicate about model quality.
• Quickly locate and interpret these metrics using the PDB Validation Slider and the summary sections of the PDB Validation Report.