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A minimum of 50 model removals makes the tested 2K39 and 6V5D contact graphs agree.

For chain A of ubiquitin PDB entries 2K39 and 6V5D, an exact finite-sample search found that a minimum of 50 model removals makes their complete majority C-alpha contact graphs agree under the stated 8 Å, residue-pair, and tie rules. A verified witness removes 50 of 116 models from 2K39 and none of 176 from 6V5D; both remaining graphs have 169 contacts, and all 2,278 labels agree. Rational certificates rule out every total below 50 for these stored coordinates and rules. Coordinate rounding within ±0.0005 Å per axis leaves the original labels fixed, while individual labels can change after model removal. This is a result for these finite deposited ensembles, not a general claim about proteins or physical state frequencies; rounding and removal were not tested jointly, and model-group membership and experimental-fit constraints remain unresolved.

ubiquitin · NMR ensembles · contact graphs · model removal · coordinate precision · exact optimization

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References

8
  1. The 2K39 and 6V5D majority contact graphs remain fixed at 8 Å within ±0.0005 Å coordinate limits sci:sha256:e12acf361757fc45ff9f7352c06904044ad64b8db876ddb067ba8eb4811192d2

    [Legacy relation: reproduces] The executed coordinate-rounding check gave the same 167 and 169 contacts, eight graph differences, and fixed majority labels for all 2,278 pairs per entry. This relation covers only the two-entry primary 8 Å result. It does not cover the full distance-limit grid.

  2. usesMean coordinates cannot give all 8 Å majority contacts with one distance limit for the specified 2K39 and 6V5D models sci:sha256:ad42441966e00d6bfcff7e90561cd6aa003e96e8967cefea9db9145af4520552

    The coordinate files and contact-count table gave data and comparison counts for all three PDB entries. All 52 manifest files passed checksum and size checks. This run checked the 6,834 primary 8 Å counts before the model-removal analysis.

  3. usesdoi:10.2210/pdb1d3z%2Fpdb

    PDB entry 1D3Z supplies the separate three-entry comparison.

  4. usesdoi:10.2210/pdb2k39%2Fpdb

    PDB entry 2K39 supplies one ensemble in the primary joint comparison.

  5. usesdoi:10.2210/pdb6v5d%2Fpdb

    PDB entry 6V5D supplies one ensemble in the primary joint comparison.

  6. doi:10.1126/science.1157092
  7. doi:10.1007/s10858-019-00288-8
  8. doi:10.1371/journal.pcbi.0040043

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