NMR Ensembles of Models: Difference between revisions
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About 11% of the entries in the [[Protein Data Bank]] were determined by nuclear magnetic resonance in solution (NMR) as of mid-2012. 88% were determined by [[X-ray crystallography]], and <1% by other methods. NMR can only be used for relatively small macromolecules (see [[#Median_Size_of_Published_NMR_Structures|below]]). | About 11% of the entries in the [[Protein Data Bank]] were determined by nuclear magnetic resonance in solution (NMR) as of mid-2012. 88% were determined by [[X-ray crystallography]], and <1% by other methods. NMR can only be used for relatively small macromolecules (see [[#Median_Size_of_Published_NMR_Structures|below]]). | ||
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NMR spectroscopy is based on the ability of an atomic nucleus with a spin of 1/2 (e.g. <sup>1</sup>H, <sup>13</sup>C, <sup>15</sup>N, <sup>31</sup>P) to adopt two different orientations in a magnetic field. | |||
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The primary data yielded by NMR analysis is mostly local and more recently global geometric information about atoms within the structure. Typically, these include distance between pairs of atoms, dihedral angles (typically backbone φ angles and some side-chain χ1 angles) and sometimes global information such as the orientation of a given bond with respect to a fixed axis of the molecule. These data are used as "restraints" to reconstruct 3D models which are compatible with the NMR data. All calculations are performed directly in the physical space, starting with a random conformation of the macromolecule, which is progressively folded to satisfy the restraints. Typically, several runs are performed, starting from different initial conformations, in order to check that the calculation converges onto a single solution. The result is thus an ensemble of models, the distribution of which gives a measure of the precision of the NMR structure. | The primary data yielded by NMR analysis is mostly local and more recently global geometric information about atoms within the structure. Typically, these include distance between pairs of atoms, dihedral angles (typically backbone φ angles and some side-chain χ1 angles) and sometimes global information such as the orientation of a given bond with respect to a fixed axis of the molecule. These data are used as "restraints" to reconstruct 3D models which are compatible with the NMR data. All calculations are performed directly in the physical space, starting with a random conformation of the macromolecule, which is progressively folded to satisfy the restraints. Typically, several runs are performed, starting from different initial conformations, in order to check that the calculation converges onto a single solution. The result is thus an ensemble of models, the distribution of which gives a measure of the precision of the NMR structure. | ||