The 2K39 ensemble has greater C-alpha distance spread for 163 of 167 selected 1UBQ contacts

For 167 C-alpha contact pairs selected from residues 1–70 of the 1UBQ crystal structure, the 2K39 ensemble had greater population standard deviation (SD) than the 6V5D ensemble for 163 pairs. The median pairwise SD ratio (2K39/6V5D) was 1.7200498882688862. Interquartile range and median absolute deviation were also greater for 163 of 167 pairs, with median ratios 1.6840004893197085 and 1.6789799213155556. In 1,000 selections of 116 6V5D models, all median pairwise SD ratios exceeded one (range 1.6793381473686402–1.8667404922167725). New Python code matched all 2,292 saved reference comparisons within the stated tolerance. Eight pairs had at least one spread-measure ratio at or below one. The analysis concerns these archived coordinates; models and pairs are dependent, equal model weights do not represent measured solution populations, and the calculations do not establish biological movement, causality, or which ensemble better describes solution behavior. The checks did not cover 1D3Z, alignment results, or figures.

ubiquitin · protein structure · C-alpha distance · distance spread · NMR ensembles · reproducibility · coordinate audit