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| Crystal structure of IRAK4 kinase domain with inhibitor |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 1.2 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 142.860 Å | b: 138.750 Å | c: 88.020 Å | α: 90.00° | β: 124.59° | γ: 90.00° |
| Resolution | 2.14 Å | Reflections | 76998 | Test set | 3869 (5.0%) | ||
| R | 0.1953 | R-free | 0.2175 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.14 Å | Reflections | 76998 | Test set | 3869 (5.0%) | ||
| Twin | false | Radiation damage | 44 | ||||
| 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 | 0.2021 | 0.1822 |
| R-free | 0.2251 | 0.2159 |
| Bond length RMS Z-score | 0.996 | 0.604 |
| Bond angle RMS Z-score | 0.865 | 0.747 |
| Model quality | ||
| Ramachandran plot normality | -1.416 44 | -1.081 53 |
| Rotamer normality | -2.552 40 | -1.263 67 |
| Coarse packing | 1.037 86 | 1.216 89 |
| Fine packing | -0.079 81 | 0.107 85 |
| Bump severity | 0.006 68 | 0.012 51 |
| Hydrogen bond satisfaction | 0.895 43 | 0.895 43 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 17 |
| Side chains built | 0 |
| Waters removed | 151 |
| Peptides flipped | 3 |
| Chiralities fixed | 0 |
| Residues fitting density better | 108 |
| Residues fitting density worse | 1 |