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![[Figure 10]](qe5008fig10mag.jpg)
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Figure 10
Comparison of residue assignments and proportions of questionable conformations in PDB/minimized and PDB/PDB-REDO models. (a) Scatter plot showing the relationship between PDC values obtained in the PDB/PDB-REDO comparison and those in the PDB/minimized comparison across the Xray694 data set. (b) Alluvial plot showing the correspondence between residue classifications in the PDB/minimized (left) and PDB/PDB-REDO (right) comparisons. The rectangular boxes represent residue categories (RCC and RDC), while the colored flows indicate transitions between categories across the two comparisons. The width of each flow is proportional to the fraction of residues undergoing the corresponding transition. (c)–(e) Exploration of the properties of residues classified based on their assignment (RDC or RCC) in both PDB/minimized and PDB/PDB-REDO comparisons. The RDC·RDC residues are those assigned as RDC in both comparisons (PDB/minimized and PDB/PDB-REDO), the RCC·RCC residues are those assigned as RCC in both comparisons, the RDC·RCC residues are those assigned as RDC in the PDB/minimized comparison and as RCC in the PDB/PDB-REDO comparison, and the RCC·RDC residues are those assigned as RCC in the PDB/minimized comparison and as RDC in the PDB/PDB-REDO comparison. (c, d) Distributions of the flexibility (c), quantified by the normalized B-factor, and the accessible surface area (d) of the four residue categories. (e) Mosaic plot illustrating the distribution of structural letters among the four residue categories. The x axis displays the 27 structural letters and the y axis displays the four residue categories. The width of the columns is proportional to the number of observations of each structural letter. The vertical length of the bars is proportional to the number of observations in the four residue categories. Pearson residuals from the χ2 test: red shades indicate overrepresented combinations (positive residuals), whereas blue shades indicate underrepresented combinations (negative residuals). The intensity of the color is proportional to the magnitude of the residuals. |
![[Figure 10]](qe5008fig10.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
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