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| Human thymidylate synthase complexed with dUMP and Raltitrexed, an antifolate drug, is in the closed conformation |
| This entry was created with PDB-REDO version 7.36 using the deposited PDB model |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 1 | a: 68.849 Å | b: 70.495 Å | c: 74.533 Å | α: 70.23° | β: 83.29° | γ: 73.28° |
| Resolution | 1.90 Å | Reflections | 93878 | Test set | 6603 (7.0%) | ||
| R | 0.2010 | R-free | 0.2440 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.90 Å | Reflections | 93878 | Test set | 6603 (7.0%) | ||
| Twin | false | Radiation damage | N/A | ||||
| 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 | 0.2060 | 0.1799 |
| R-free | 0.2418 | 0.2123 |
| Bond length RMS Z-score | 0.290 | 0.421 |
| Bond angle RMS Z-score | 0.637 | 0.702 |
| Model quality | ||
| Ramachandran plot normality | -1.983 30 | -0.608 64 |
| Rotamer normality | -2.344 51 | -0.185 90 |
| Coarse packing | -0.828 22 | -0.720 26 |
| Fine packing | -0.412 73 | -0.089 81 |
| Bump severity | 0.048 20 | 0.063 15 |
| Hydrogen bond satisfaction | 0.899 49 | 0.892 40 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 25 |
| Side chains built | 0 |
| Waters removed | 31 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 19 |
| Residues fitting density worse | 0 |