NMR Ensembles of Models: Difference between revisions
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===Meaning of the Variation Between Models=== | ===Meaning of the Variation Between Models=== | ||
The '''variation between models''' in the ensemble can mean either of two things. The variation can represent actual '''flexibility and thermal motion''' that occurred during the NMR measurements in solution, typically at room temperature. Alternatively, the variation can simply mean '''uncertainty in the atomic positions''', namely, that an inadequate number of restraints were available to determine the positions of some atoms. Unfortunately, there is nothing comparable to the [[B value]] or [[Temperature value]] that quantitates the uncertainty of the position of each atom in crystallographic results. | The '''variation between models''' in the ensemble can mean either of two things. The variation can represent actual '''flexibility and thermal motion''' that occurred during the NMR measurements in solution, typically at room temperature. Alternatively, the variation can simply mean '''uncertainty in the atomic positions''', namely, that an inadequate number of restraints were available to determine the positions of some atoms. Unfortunately, there is nothing comparable to the [[B value]] or [[Temperature value]] that quantitates the uncertainty of the position of each atom in crystallographic results. Specific NMR relaxation experiments can however be used to measure the dynamics of individual atoms, mainly backbone amide groups, as the relaxation of the NMR signal is indeed dependent on the internal motions of the molecule. When these NMR relaxation data are available, they can be used to determine '''order parameters''', which are strongly correlated with the [[B value]]s of the crystallographic structures. These can be used to distinguish between intrinsic flexibility and uncertainty due to lack of constraints. When relaxation data is not available, the only way to find out what the meaning of the variation between models is to contact the experimenters who authored the published ensemble of models. | ||
Protein chains commonly have more variation between models at the ends than in the middle. An example is [[2yru]]. | Protein chains commonly have more variation between models at the ends than in the middle. An example is [[2yru]]. | ||
