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NMR vs X-Ray Structures

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In the PDB, it’s possible to find structures solved by X-ray crystallography and NMR (around 15% of the deposited structures). Structures solved by X-ray crystallography are considered to be of higher quality, and thus, when available are preferable to use. However, it’s not always easy or possible to crystallize the proteins. 

X-ray solved structures are not free of error. Due to crystal packing effectes, macromolecules' structure might suffer deformations which are eventually reflected in the deposited structure.

The most apparent difference one finds between both types of structures is that while X-ray solved ones are single, NMR derived structures are normally deposited as an ensemble, due to the determining experimental factors. X-ray structures have also an associated "quality measurement":  the resolution. This is given in Angstrom. If there are several structures available for the same macromolecule, one should prefer one with a resolution less than 2.5 Å, which is considered good enough as to use the structure for applications requiring high quality such as computational protein-ligand docking. Another interesting difference is that X-ray structures do not contain hydrogens (as they cannot be “seen” in the experiment) in contrast to NMR structures, but do normally contain water molecules that have fixed to the crystal structure (some of theses might play a role in the function of the protein).

You can learn more about the limitations of the X-ray difraction as a technique for solving macromolecular structures.

In this module we will explore the aforementioned differences. We will perform global and local structural alignments of proteins solved by both techniques. The concept of RMSD to assess differences between different conformations will be introduced. The capabilities to do distance and angle measurements in PyMOL will be explored. Some of these tasks, are suitable for automation: we will learn how to use the scripting capabilities in PyMOL to increase productivity in repetitive tasks. Finally, the concept of “scenes” will be explored, as the basis for making small movies.

In the mean time, you can find here ans interesting collection of references dealing with differences between X-Ray and NMR solved structures

A general insight on the topic can also be found on the PDB website.

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