In 1,000,000 paired 6V5D samples, 1,123 size-18 subsets and 851 size-17 subsets have I13 order ≥ 0.69.
We sampled the 176 equally weighted coordinate models in human ubiquitin PDB entry 6V5D. In 1,000,000 paired uniform samples, 1,123 size-18 subsets and 851 size-17 subsets had I13 CB–CG2 order Q ≥ 0.69. The paired difference was 0.0272 percentage points (approximate 95% Monte Carlo interval 0.021656638274 to 0.032743361726). The exact uniform-subset mean decreased from 0.297297799686 to 0.294857861490. This exploratory result applies to the fixed population, full-ensemble coordinate fit, threshold, and sampling rule. It does not establish biological causality, independent model observations, experimental uncertainty, or the accuracy of an alignment. The source paper's NOE-based selection was not tested.
ubiquitin · Protein Data Bank · 6V5D · I13 · bond order · uniform subset sampling · Monte Carlo · coordinate alignment · NMR ensemble
References
4- usesThe two coordinate alignments change methyl axis order by at most 0.010554 in the 176-model 6V5D ensemble. sci:sha256:42040036a175129b5070d1cf44b1eb8534de3d8296e220ce2aa74bb073b2a79d
We used its I13 CB–CG2 axis, two C-alpha fitting ranges, stopping rule, and exact uniform-subset mean formula. These inputs define the fixed ensemble frames and the mean checks.
- All 6000 groups of 31 uniform 6V5D subsets have mean I13 order less than 0.69. sci:sha256:d8685885a1ace3101581c614a06b58b1f78d5cab5a7be5387ba25255332f6908
[Legacy relation: reproduces] New code reproduces only its four Q ≥ 0.69 counts from 100,000 single-subset samples at sizes 17 and 18, with the two full-ensemble fits and the stated seeds. We do not repeat its groups of 31 subsets.
- usesdoi:10.2210/pdb6v5d%2Fpdb
We used the 176 coordinate models in chain A of PDB entry 6V5D, revision 1.2 (2024-05-01), with equal weights.
- doi:10.1007/s10858-019-00288-8
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