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![[Figure 2]](kk5067fig2mag.jpg)
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Figure 2
Bias-minimized electron density for an improbable peptide. The left map is a REFMAC (Murshudov et al., 1997  ) 2mFo–DFc omit map (i.e. the Sb2 peptide omitted in the model) reconstructed from σA-based maximum-likelihood coefficients (Read, 1986). The map contoured at the 0.8σ density level (blue) shows no trace of the peptide (stick model, residues 77–84 shown in the figure). Density reconstruction indicates a possible water network in the vicinity of the binding site, but no trace of the peptide. The strong density (red, 5σ) for the also omitted Zn atom is emphasized by the red circle. The electron density reconstructed by other methods looks the same (Rupp & Segelke, 2001; Breidenbach & Brunger, 2004). Compare the corresponding electron-density real-space correlation coefficient (Rupp, 2009, Fig. 13-7). The right panel shows a CNS (Brunger, 2007) difference map reconstructed from cross-validated σA Fo–Fc maximum-likelihood coefficients. Both the Sb2 peptide and the Zn ion were omitted in the map calculations. No positive difference density for the peptide at a 2σ density level can be found in the Fo–Fc difference map. Note in contrast the strong positive difference density (blue, cyan) for the omitted Zn ion in the difference map. Negative difference density in red, positive difference density in blue (which should reveal Sb2 peptide density, if it were present). Structure factor amplitudes and model from obsolete PDB entry 3g94
. Image created using Xtalview (McRee, 1999) and rendered with Raster3D (Merritt & Bacon, 1997). |
![[Figure 2]](kk5067fig2.jpg)
 | JOURNAL OF APPLIED CRYSTALLOGRAPHY |
ISSN: 1600-5767
