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![[Figure 7]](ji5028fig7mag.jpg)
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Figure 7
Analysis of initial and refined models of two Hom targets using the DAQ(AA) score. (a) PDB entry 6l54 chain C built from EMDB entry EMD-0837 contained regions that are inconsistent with the other protein model, PDB entry 6z3r chain C from EMDB entry EMD-11063. This region is shown in magenta in the leftmost structure and is detected as negative DAQ(AA) scores, as shown in red with thick tubes in the model second from the left. The refined model is shown on the right. It has an overall positive score (blue). The four squares provide magnified views of residues in the inconsistent region before and after refinement by DAQ-refine. EMDB entry EMD-0837 used for refinement is shown as a mesh in the top squares. The lower squares show the map of the reference homologous structure (EMDB entry EMD-11063). The DAQ score plots have gaps at missing residues in the initial model (PDB entry 6l54 chain C). In the enlargements, Asp423 and Glu425 in pink are the conformations of these two residues in the initial model, whereas those in cyan are the results of DAQ-refine. Those in orange are conformations in the reference structure, PDB entry 6z3r chain C. (b) Local refinement of PDB entry 5lc5 chain N, which was built from EMDB entry EMD-4032, in comparison with PDB entry 6zkm chain N, which was derived from EMDB entry EMD-11254. The enlargements highlight Met334 and Leu336 in an inconsistent region between the two entries. The squares show the maps of the initial structure and the reference homologous structure (top, EMD-4032; bottom, EMD-11254) as meshes. In the refined model, Met334 and Leu336 were shifted to the corresponding positions in PDB entry 6zkm chain N and the DAQ(AA) score improved (red arrows in the plots). |
![[Figure 7]](ji5028fig7.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
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