ArticleProtein science : a publication of the Protein Society2017
Systematic analysis of residual density suggests that a major limitation in well-refined X-ray structures of proteins is the omission of ordered solvent.
Article in Protein science : a publication of the Protein Society, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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5 citing papers in PubMed.
- Visualization of H atoms in the X-ray crystal structure of photoactive yellow protein: Does it contain low-barrier hydrogen bonds?Protein science : a publication of the Protein Society · 2019Article
- Crystallographic evidence for two-metal-ion catalysis in human pol η.Protein science : a publication of the Protein Society · 2019Article
- Misreading chaperone-substrate complexes from random noise.Nature structural & molecular biology · 2018Article
- Determination of chemical identity and occupancy from experimental density maps.Protein science : a publication of the Protein Society · 2018Article
- Chlorophyll a with a farnesyl tail in thermophilic cyanobacteria.Photosynthesis research · 2017Article
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Abstract
In the residual electron density map of a fully refined X-ray protein model, there should be no peaks arising from modeling errors or missing atoms. Any residual peaks that do occur should be contributed by random residual intensity differences between the model and the data. If the model is incomplete (i.e., some atoms are missing), there will be more positive peaks than negative ones. On the other hand, if the model includes inappropriately located atoms, there will be an excess of negative peaks. In this study, random residual peaks are quantified using the probability density function P(x), which is defined as the probability for a peak having peak height between x and x + dx. It is found that P(x) is single-exponential and symmetric for both positive and negative peaks. Thus, P(x) can be used to discriminate residual peaks contributed by random noise in complete models from residual peaks being attributable to modeling errors in incomplete models. For a number of representative structures in the PDB it is found that P(x) has far more large (greater than 5 sigma) positive peaks than large negative peaks. This excess of large positive peaks suggests that the main defect in these refined structures is the omission of ordered water molecules.
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