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q-bio.BM · Biomoleculesq-bio.QM · Quantitative Methodsphysics.bio-ph · Biological Physics

Crystal B-profile choice changes chain-level ubiquitin ensemble correlation ordering

In a six-entry, nonrandom ubiquitin crystal panel, changing the deposited crystal C-alpha B profile while holding ensemble coordinates and alignment fixed reversed the Spearman ordering of 6V5D versus 2K39 in 2 of 12 chains. The chain-level difference ranged from -0.054659 to +0.121250, while entry-mean profiles gave positive differences for all six entries. Fresh code reproduced the prior 12-row correlation table on the same archived inputs (maximum absolute difference 2.22e-16). These are conditional observations about deposited models, not an ensemble quality ranking or a measure of biological dynamics. Chain choice, aggregation, and correlation metric matter; the small descriptive panel does not control temperature, packing, zinc, resolution, or refinement, and provides no significance test or causal estimate.

ubiquitin · protein ensembles · B factors · crystal structures · NMR · Spearman correlation · reproducibility · sensitivity analysis

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References

18
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    [Legacy relation: reproduces] Fresh code reproduces its complete twelve-row correlation table using its four checksum-verified archived structure snapshots (maximum absolute difference 2.22e-16). This supplies the baseline for a new five-entry crystal B-profile sensitivity comparison; no original biological or kinetic claim is replicated.

  2. usesdoi:10.2210/pdb1d3z%2Fpdb

    This deposited PDB entry supplies coordinates or B annotations used in the described comparison; bundled archive revision and hashes are recorded in original/data/manifest.json.

  3. doi:10.1021/ja9812610
  4. usesdoi:10.2210/pdb1ubq%2Fpdb

    This deposited PDB entry supplies coordinates or B annotations used in the described comparison; bundled archive revision and hashes are recorded in original/data/manifest.json.

  5. doi:10.1016/0022-2836(87)90679-6
  6. usesdoi:10.2210/pdb2k39%2Fpdb

    This deposited PDB entry supplies coordinates or B annotations used in the described comparison; bundled archive revision and hashes are recorded in original/data/manifest.json.

  7. doi:10.1126/science.1157092
  8. usesdoi:10.2210/pdb3ehv%2Fpdb

    This deposited PDB entry supplies coordinates or B annotations used in the described comparison; bundled archive revision and hashes are recorded in original/data/manifest.json.

  9. doi:10.1039/b813463d
  10. usesdoi:10.2210/pdb3n30%2Fpdb

    This deposited PDB entry supplies coordinates or B annotations used in the described comparison; bundled archive revision and hashes are recorded in original/data/manifest.json.

  11. doi:10.1002/chem.201001617
  12. usesdoi:10.2210/pdb3ons%2Fpdb

    This deposited PDB entry supplies coordinates or B annotations used in the described comparison; bundled archive revision and hashes are recorded in original/data/manifest.json.

  13. doi:10.1002/pro.584
  14. usesdoi:10.2210/pdb4xok%2Fpdb

    This deposited PDB entry supplies coordinates or B annotations used in the described comparison; bundled archive revision and hashes are recorded in original/data/manifest.json.

  15. doi:10.1038/ncomms9361
  16. usesdoi:10.2210/pdb4xol%2Fpdb

    This deposited PDB entry supplies coordinates or B annotations used in the described comparison; bundled archive revision and hashes are recorded in original/data/manifest.json.

  17. usesdoi:10.2210/pdb6v5d%2Fpdb

    This deposited PDB entry supplies coordinates or B annotations used in the described comparison; bundled archive revision and hashes are recorded in original/data/manifest.json.

  18. doi:10.1007/s10858-019-00288-8

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