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![[Figure 4]](jm5003fig4mag.jpg)
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Figure 4
Bulk-solvent parameters. Two-dimensional density function of the bulk-solvent parameters kmask/Bmask derived from 70 481 entries deposited in the PDB for which refinement data could reliably be extracted. Values for the mean solvent density kmask and smearing factor Bmask were computed with PHENIX (Adams et al., 2010  ). The plot is limited to PDB entries with Rwork between 0.05 and 0.30, only positive values for kmask, measurements of Bmask of less than 300 and a solvent content of at least 5%. The density function was constructed using a two-dimensional kernel density estimation with an axis-aligned bivariate normal kernel and has been normalized to a maximum value of 1. Isocontour lines are plotted as solid lines at regularly spaced intervals of size 0.2. Box plots show the extents of the kmask and Bmask distributions; the median is indicated by a thick line in the grey box, which represents the interval from the lower to the upper quartile, and whiskers extend to data points not more extreme than 1.5 times the interquartile range. The sample median of kmask equals 0.36 (0.04) e Å−3 and for Bmask the sample median is 42.4 Å2. The distribution of Bmask has a small tail towards higher values, which is expressed by its sample skewness of 3.2, whereas the kmask distribution appears to be much more symmetric about its mean, with a sample skewness of 0.43. This plot does not show 2.7% of Bmask entries and 1.7% of kmask data, which are located outside of the limits of the axes. This figure was generated with matplotlib (Hunter, 2007). |
![[Figure 4]](jm5003fig4.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
