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Figure 4
Log-likelihood gradient (LLG) maps, contoured at +6 (cyan contours) and −6 (magenta contours) times the r.m.s. deviation of the LLG map; this figure was prepared using CCP4mg (Potterton et al., 2004BB18). (a) Using data from a bromide soak of the human acyl protein thioesterase I (Devedjiev et al., 2000BB5), the program HySS (Grosse-Kunstleve & Adams, 2003BB6) found a substructure of 21 bromide ions. After refinement in Phaser (in which the occupancies refined close to zero for six of the sites), an LLG map was computed. Density is shown for the top two sites in the context of the final protein model, which was not consulted in the calculation. At the convergence of LLG completion, the substructure contained 40 sites. (b) A model of the four Yb atoms in the Yb-substituted mannose-binding protein (Burling et al., 1996BB2) was refined in Phaser with isotropic B factors before computing an LLG map, which illustrates the positive and negative features that indicate anisotropic motion.

Journal logoBIOLOGICAL
ISSN: 1399-0047
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