Ubiquitin ensemble–B-factor agreement varies with tail inclusion and alignment mask

This fixed-case descriptive analysis compares C-alpha coordinate spread in three deposited ubiquitin ensembles with the C-alpha B-factor profile of one crystal structure (1UBQ). All 303 coordinate models, including the crystal, have the same complete 76-residue chain A sequence. With models fitted on residues 1–70, Spearman correlations evaluated over residues 1–76 versus 1–70 were 0.344161 versus 0.161494 for 1D3Z, 0.634855 versus 0.533121 for 2K39, and 0.700256 versus 0.617070 for 6V5D. Fitting on residues 1–76 while evaluating residues 1–70 gave 0.315131, 0.523410, and 0.610508. For 1D3Z, median body RMSF changed from 0.084745 Å to 0.279052 Å with this alignment change. The body-only Pearson MSD/B ordering of 2K39 and 6V5D differed from their Spearman ordering. Tail residues 71–76 accounted for 99.0978%, 84.3245%, and 82.3486% of summed coordinate MSD in 1D3Z, 2K39, and 6V5D. Random ten-model subsets gave conditional sensitivity ranges, not biological confidence intervals. These observations describe the selected archive models and one crystal reference. They do not estimate biological motion, identify the more physically faithful ensemble, independently replicate the source studies, or test their original validation and kinetic claims. B-factors include static disorder, lattice, and refinement effects; 6V5D includes crystal-derived model subsets, and 2K39 and 6V5D are not independent. See the full methods, results, checks, and limitations in README.md.

ubiquitin · protein structure · NMR ensemble · B-factors · RMSF · alignment sensitivity · coordinate variance · structural bioinformatics