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![[Figure 5]](tz5099fig5mag.jpg)
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Figure 5
Peak-classification examples from six different structures. Peaks are shown as black spheres, macromolecular components are coloured by element (carbon in brown, oxygen in red, nitrogen in blue, hydrogen omitted) and posited models are shown in green. Electron density is shown as a mesh (Fo − Fc in red and 2Fo − Fc in grey contoured at 3.0σ and 1.0σ, respectively, unless noted otherwise). Top row: peaks from training data with nominally incorrect PeakProbe classifier predictions likely to be mislabelled in the PDB. Bottom row: peaks not associated with any existing solvent models but strongly predicted to belong to the class indicated by PeakProbe. Details are as follows. (a) PDB entry 4aqp (2.45 Å); the peak is water A2001 predicted to be a sulfate (modelled in green). Crystals were grown in the presence of the sulfate pseudo-analog 2-(N-morpholino)ethanesulfonic acid (MES). (b) PDB entry 2xrz (2.20 Å); the central peak is water B2012. Of the six peaks shown, four were strongly predicted to be heterogen. Crystals were grown in the presence of polyethylene glycol, a two-conformer model for which is shown as a point of reference in green. (c) PDB entry 2p3i (1.75 Å); the peak is the central S atom of sulfate A3000 (shown in cyan) and was strongly predicted to be water. (d) PDB entry 1mh3 (2.10 Å); the peak is adjacent to the terminal N atom of lysine A500 and was strongly predicted to be a sulfate (modelled in green). (e) PDB entry 2wjj (2.41 Å); four peaks are shown bracketed between the side chains of glutamate A95 and lysine A132, all strongly predicted to be heterogen. Crystallization conditions give no indications of likely models. (f) PDB entry 3zm4 (2.37 Å), Fo − Fc density contoured at 5.0σ, 2Fo − Fc density at 1.8σ; the peak is at a special position adjacent to aspartate A65 and is strongly predicted to be a metal. Crystals were grown in the presence of 0.2 M Ca2+ and the crystal lattice appears to be held together by electrostatic attraction between the acidic side chains shown and an unmodelled cation. |
![[Figure 5]](tz5099fig5.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
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