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![[Figure 5]](rr5162fig5mag.jpg)
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Figure 5
Robustness to outliers when performing atomic model refinement using external restraints. The re-refined atomic model corresponding to the RAD51 filament (PDB entry 5jzc, EMDB entry EMD-8183; Short et al., 2016  ), as shown in Fig. 4(a), is displayed coloured green. External restraints were generated using ProSMART using the homologous structural model derived using MX (PDB entry 1n0w; Pellegrini et al., 2002) as a reference. The homologous model 1n0w is shown coloured brown superposed onto 5jzc. (a) The red colouring of the restraints reflects differences in the rotameric state of the aligned functional tyrosine between the target and reference models (Tyr293 in 5jzc, Tyr301 in 1n0w). Map density is clearly visible; this side chain is oriented acceptably in the original model, so it would be undesirable for the external restraints to pull this side chain into the conformation observed in the homologous model. (b) The model after real-space re-refinement with external restraints in Coot (as shown in Fig. 4b) is coloured blue. Owing to the use of robust estimation, which restricts the influence of outliers, the tyrosine side chain retains its original conformation rather than being pulled out of the map and into the rotameric state observed in the homologous model. However, the geometry of the backbone in this region is improved, adopting a similar conformation to the homologous model as appropriate. Following such injection of prior structural information, the typical protocol would then be to perform full-model refinement using REFMAC5 with jelly-body restraints, which would allow the model to relax into the density whilst ensuring refinement stability. |
![[Figure 5]](rr5162fig5.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
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