Electron density maps: Difference between revisions
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An "all features" map, 2Fo-Fc, is the best way to calculate an estimate of the true electron density from diffraction data and atomic model. (It is called 2Fo-Fc because the calculation involves combining the observed diffraction data, Fo, with the expected diffraction data, Fc, in a way that gives the least-biased result). Typically contoured at '''1 sigma''', it shows how well the observed density fits around the atomic model<ref name="silvaggi" />. Ideally, a feature present in the crystal but not yet included in the model will show up with '''half the signal strength''' compared to features present in the crystal and included in the model. Likewise, spurious features included in the model will show up with half signal strength. This difference between real density and 2Fo-Fc density is called model bias, and is related to using the model (and the experimental data) to judge the correctness of the model, a bit of a circular argument. | An "all features" map, 2Fo-Fc, is the best way to calculate an estimate of the true electron density from diffraction data and atomic model. (It is called 2Fo-Fc because the calculation involves combining the observed diffraction data, Fo, with the expected diffraction data, Fc, in a way that gives the least-biased result). Typically contoured at '''1 sigma''', it shows how well the observed density fits around the atomic model<ref name="silvaggi" />. Ideally, a feature present in the crystal but not yet included in the model will show up with '''half the signal strength''' compared to features present in the crystal and included in the model. Likewise, spurious features included in the model will show up with half signal strength. This difference between real density and 2Fo-Fc density is called model bias, and is related to using the model (and the experimental data) to judge the correctness of the model, a bit of a circular argument. | ||
:The '''example at right''' shows the first report, in 2021, of a new kind of covalent protein crosslink, a [[Lysine-cysteine NOS bonds|lysine-cysteine NOS bond]] between the sidechains of the two amino acids in [[6zx4]]<ref>PMID: 33953398</ref>. Crystal structures reported before the recognition of this type of crosslink will have overlooked the oxygen atom, as appears likely the case for [[3u7z]] published in 2011. | :The '''example at right''' shows the first report, in 2021, of a new kind of covalent protein crosslink, a [[Lysine-cysteine NOS bonds|lysine-cysteine NOS bond]] between the sidechains of the two amino acids in [[6zx4]]<ref>PMID: 33953398</ref>. Crystal structures reported before the recognition of this type of crosslink will have overlooked the oxygen atom, as appears likely the case for [[3u7z]] published in 2011. In contrast, the map shows clearly the absence of an oxygen between the nitrogen and sulfur in [[6vb2]] (similar N-S distances of 2.6-2.7 Å and similar resolutions of 1.3-1.4 Å). | ||
2Fo-Fc maps are most useful in an intermediate stage of model building, when the model is already quite good but still missing major features (such as well-defined side-chains). There are more sophisticated tools (called omit maps<ref name="silvaggi" />) in the final stages of refinement to complete the model in less obvious areas. At the end of the refinement, the 2Fo-Fc map should not reveal any glaring omissions but might show weakness in areas of the model that are less well defined (typical examples are the amino and carboxy termini, flexible loops, glycosylation sites, weakly bound ligands and water molecules). Likely errors are represented by (i) substantial density containing no atom, or (ii) atoms with little or no density. | 2Fo-Fc maps are most useful in an intermediate stage of model building, when the model is already quite good but still missing major features (such as well-defined side-chains). There are more sophisticated tools (called omit maps<ref name="silvaggi" />) in the final stages of refinement to complete the model in less obvious areas. At the end of the refinement, the 2Fo-Fc map should not reveal any glaring omissions but might show weakness in areas of the model that are less well defined (typical examples are the amino and carboxy termini, flexible loops, glycosylation sites, weakly bound ligands and water molecules). Likely errors are represented by (i) substantial density containing no atom, or (ii) atoms with little or no density. | ||
