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| Crystal structure of ITK in complex with compound 8 [4-(carbamoylamino)-1-(7-propoxynaphthalen-1-yl)-1H-pyrazole-3-carboxamide] |
| This entry was created with PDB-REDO version 8.07 using the deposited PDB model version 1.2 |
| From original header | |||||
|---|---|---|---|---|---|
| Spacegroup | P 1 21 1 | a: 40.523Å b: 68.900Å c: 68.900Å | α: 90.00° β: 106.88° γ: 90.00° | ||
| Resolution | 1.85 Å | Reflections | 21479 | Test set | 1142 (5.3%) |
| R | 0.1874 | R-free | 0.2324 | ||
| According to PDB-REDO | |||||
| Resolution | 1.85 Å | Reflections | 21479 | Test set | 1142 (5.3%) |
| Twin | false | Radiation damage | 29 | ||
| PDB-REDO files | |||||
| Re-refined and rebuilt structure |
Re-refined (only) structure
|
All files
(compressed) |
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| Links | |||||
| PDBe | RCSB PDB | Proteopedia | |||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.1817 | 0.1757 |
| R-free | 0.2218 | 0.2216 |
| Bond length RMS Z-score | 0.953 | 0.217 |
| Bond angle RMS Z-score | 0.784 | 0.469 |
| Model quality | ||
| Ramachandran plot normality | -0.031 81 | 0.055 83 |
| Rotamer normality | -1.252 67 | 0.079 91 |
| Coarse packing | 0.418 67 | 0.438 68 |
| Fine packing | -0.967 54 | -0.939 56 |
| Bump severity | 0.001 90 | 0.001 90 |
| Hydrogen bond satisfaction | 0.922 79 | 0.918 74 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 7 |
| Side chains built | 0 |
| Waters removed | 16 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 1 |
| Residues fitting density worse | 0 |