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- Introduction to model quality assessment
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- Key takeaways
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Key metrics based on experimental data fit
These metrics evaluate how well the atomic coordinates of the model explain the experimental data collected.
Resolution (for X-ray and cryoEM)
Resolution, primarily used in X-ray crystallography and cryo-EM, is a fundamental measure of the level of fine detail that can be distinguished in the experimental data and, consequently, in the resulting structural model. It indicates the smallest distance between two points that can be resolved as separate entities.
Resolution is expressed in Ångströms (Å), where 1 Å = 10-10 meters. Lower values signify higher resolution, meaning you can distinguish finer details. For example, a covalently bonded carbon atom is approximately 1.5 Å in diameter. Therefore, a structure determined at 1.5 Å resolution has a higher level of detail, potentially allowing individual atoms to be clearly distinguished. In contrast, a 3.0 Å resolution structure provides less detail.
Higher resolution data generally allows for more precise placement of atoms in the model and clearer visualisation of individual atoms and their interactions, typically leading to more accurate and reliable models. Lower resolution structures can still provide valuable information about the overall fold and shape of the macromolecule, but fine details, side-chain conformations, and flexible loop regions might be less reliable.
The effect of X-ray data resolution on visible detail in electron density maps, illustrated by Tyrosine 103 of Myoglobin. This figure compares the electron density maps and fitted atomic models for the same tyrosine residue (Tyr103) in myoglobin structures determined at progressively lower resolutions.
It is important to note that resolution figures from different techniques (e.g., X-ray vs. cryo-EM) are calculated differently and are not always directly comparable in terms of the level of detail visible throughout the entire model. Local variations in data and model quality can exist even in structures reported at high nominal resolution.
Hands-on activity: Comparing resolution and detail
Goal: To visually understand how resolution impacts the level of detail in an X-ray structure.
Instructions:
- Go to the PDBe website (www.ebi.ac.uk/pdbe/).
- Find the PDB entry 1A6M. What is its reported resolution?
- Now, find the PDB entry 108M. What is its reported resolution?
- Using the Mol* viewer on the PDB page for each entry, visually compare a specific amino acid, like Tyr103. Can you observe differences in the clarity of the side-chain density and atomic positions between the two resolutions?