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![[Figure 8]](qn5003fig8mag.jpg)
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Figure 8
Ribosomal subunit (PDB entry 3pio) coloured by ZbpG, illustrating the effects of the Stac restraint model. Protein is coloured dark grey. (a) Structure model as available in the PDB. (b) Structure as obtained by PDB-REDO. (c) Protein–RNA interface site of A/215Trp and X/1582A. 2mFo − DFc density map in blue at 1.15σ, mFo − DFc difference map in green and red at 3.0σ. For clarity, maps were oversampled with grid size 0.5. (d) The same protein–RNA site in PDB-REDO, keeping the π-stacking but obtaining a better fit with the electron density and a hydrogen bond between the NE1 atom of A/215Trp and the OP2 atom of X/777A. (e) Overlay of the PDB model with the PDB-REDO model, both coloured byZbpG, for base pairs X/57G–X/68C and X/58C–X/67G, which became more normal in the PDB-REDO model. (f) Overlay of the PDB with the PDB-REDO model, both coloured by ZbpG, of base pair X/1538A–X/1485U, which became more normal in the PDB-REDO model. |
![[Figure 8]](qn5003fig8.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
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