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| A Src-like Inactive Conformation in the Abl Tyrosine Kinase Domain |
| This entry was created with PDB-REDO version 8.01 using the deposited PDB model version 1.4 |
| From original header | |||||
|---|---|---|---|---|---|
| Spacegroup | P 41 21 2 | a: 88.457Å b: 88.457Å c: 235.625Å | α: 90.00° β: 90.00° γ: 90.00° | ||
| Resolution | 3.12 Å | Reflections | 17057 | Test set | 925 (5.4%) |
| R | 0.2490 | R-free | 0.3080 | ||
| According to PDB-REDO | |||||
| Resolution | 3.12 Å | Reflections | 17057 | Test set |
867 (5.1%)
New test set, PDB-REDO compensated for this
|
| Twin | false | Radiation damage | N/A | ||
| PDB-REDO files | |||||
| Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
|||
| Links | |||||
| PDBe | RCSB PDB | Proteopedia | |||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.2916 | 0.1966 |
| R-free |
0.2958
R-free was considered biased, the
estimated unbiased R-free was used
|
0.2431 |
| Bond length RMS Z-score | 0.378 | 0.514 |
| Bond angle RMS Z-score | 0.768 | 0.784 |
| Model quality | ||
| Ramachandran plot normality | -6.337 2 | -2.420 23 |
| Rotamer normality | -4.773 17 | -2.797 43 |
| Coarse packing | -0.823 22 | -0.489 37 |
| Fine packing | -1.651 25 | -0.572 69 |
| Bump severity | 0.132 8 | 0.022 37 |
| Hydrogen bond satisfaction | 0.819 7 | 0.587 0 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 7 |
| Side chains built | 8 |
| Waters removed | 0 |
| Peptides flipped | 8 |
| Chiralities fixed | 0 |
| Residues fitting density better | 57 |
| Residues fitting density worse | 0 |