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| Crystal structure of human hypoxanthine-guanine phosphoribosyltransferase in complex with 6-fluoro-3-hydroxy-2-pyrazinecarboxamide (T-705) ribose-5'-monophosphate |
| This entry was created with PDB-REDO version 8.07 using the deposited PDB model version 1.2 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | I 2 2 2 | a: 46.858 Å | b: 73.400 Å | c: 73.400 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
| Resolution | 2.73 Å | Reflections | 5280 | Test set | 528 (10.0%) | ||
| R | 0.2481 | R-free | 0.2784 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.73 Å | Reflections | 5280 | Test set | 528 (10.0%) | ||
| 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 | 0.2572 | 0.2539 |
| R-free | 0.2961 | 0.3088 |
| Bond length RMS Z-score | 0.762 | 0.333 |
| Bond angle RMS Z-score | 0.544 | 0.520 |
| Model quality | ||
| Ramachandran plot normality | -4.743 5 | -3.810 10 |
| Rotamer normality | -3.940 19 | -3.772 21 |
| Coarse packing | -0.497 27 | -0.442 29 |
| Fine packing | -2.095 12 | -1.754 22 |
| Bump severity | 0.041 21 | 0.043 20 |
| Hydrogen bond satisfaction | 0.849 13 | 0.873 24 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 2 |
| Side chains flipped | 7 |
| Waters removed | 1 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |