S1 Fig. Compositional Distribution of Residue Categories in Structural Determination Methods.

The figure displays the counts of residues classified as “Modeled” (<b>left</b>), “Hard missing” (<b>middle</b>), and “Soft missing” (<b>right</b>) across various structural experiments, including X-ray (<b>blue</b>), SPA (<b>orange</b>), and Tomo (<b>yellow</b>). The median counts of “Modeled” residues per protein are 242 for X-ray, 190 for SPA, and 179 for Tomo. For “Hard missing” residues, the median counts are 5 for X-ray, 25 for SPA, and 11 for Tomo. Median counts for “Soft missing” residues are not reported. <b>S2 Fig. Distribution of Residue Scores in Different Experimental Methods.</b> (A) The distribution of pLDDT residue scores (ranging from 0 to 100) across the “Modeled”, “Hard missing”, and “Soft missing” groups is presented for X-ray, Single-Particle Analysis (SPA), and Tomography (Tomo) experiments. In the X-ray dataset, the “Modeled” group shows the highest median pLDDT score at 97.1, followed by the “Soft missing” group at 84.4 and the “Hard missing” group at 55.5. For the SPA dataset, the medians are 92.7 for “Modeled”, 86.7 for “Soft missing”, and 54.5 for “Hard missing”. In the Tomo dataset, medians are 91.5 for “Modeled”, 88.6 for “Soft missing”, and 52.3 for “Hard missing”. B) The distribution of IUPred scores (ranging from 0 to 1, with scores over 0.5 indicating disorder) is shown for the same groups and experimental methods. In the X-ray experiment, the “Modeled” group has the lowest median IUPred score at 0.2, followed by “Soft missing” at 0.29 and “Hard missing” at 0.38. In SPA, the median IUPred scores are 0.19 for “Modeled”, 0.23 for “Soft missing”, and 0.43 for “Hard missing”. In Tomo, the scores are 0.2 for “Modeled”, 0.32 for “Soft missing”, and 0.42 for “Hard missing”. These findings highlight distinct score distributions across experimental methods and residue categories. <b>S1 Table.</b> Distribution of residues classified by types from different methods. <b>S2 Table.</b> Composition of amino acid residues for each dataset. <b>S3 Table.</b> Composition of structured and unstructured amino acids from this study. <b>S4 Table.</b> Prediction scores of “Hard missing” residues by different models in regions from X-ray dataset. <b>S5 Table.</b> Prediction scores of “Hard missing” residues by different models in regions from SPA dataset. <b>S6 Table.</b> Prediction scores of “Hard missing” residues by different models in regions from Tomo dataset. (DOCX)