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| Co-crystal structure of caPCNA bound to AOH1160 derivative 1LE |
| This entry was created with PDB-REDO version 8.12 using the deposited PDB model version 1.5 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | H 3 | a: 197.145 Å | b: 197.145 Å | c: 126.979 Å | α: 90.00° | β: 90.00° | γ: 120.00° |
| Resolution | 2.81 Å | Reflections | 44861 | Test set | 2023 (4.5%) | ||
| R | 0.1983 | R-free | 0.2404 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.81 Å | Reflections | 44861 | Test set | 2023 (4.5%) | ||
| Twin | false | Radiation damage | 70 | ||||
| PDB-REDO files | |||||||
| Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
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| Links | |||||||
| PDBe | RCSB PDB | 3D bionotes | Proteopedia | ||||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.2173 | 0.1933 |
| R-free | 0.2487 | 0.2274 |
| Bond length RMS Z-score | 0.755 | 0.664 |
| Bond angle RMS Z-score | 0.880 | 0.773 |
| Model quality | ||
| Ramachandran plot normality | -2.476 23 | -1.244 49 |
| Rotamer normality | -5.811 5 | -3.297 28 |
| Coarse packing | 1.539 94 | 1.795 96 |
| Fine packing | -0.703 64 | -0.167 79 |
| Bump severity | 0.023 34 | 0.018 40 |
| Hydrogen bond satisfaction | 0.874 24 | 0.874 24 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 14 |
| Side chains built | 0 |
| Waters removed | 0 |
| Peptides flipped | 2 |
| Chiralities fixed | 0 |
| Residues fitting density better | 12 |
| Residues fitting density worse | 0 |