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The crystal structure of human abl1 T315I gatekeeper mutant kinase domain in complex with axitinib |
This entry was created with PDB-REDO version 8.04. |
From original header | |||||||
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Spacegroup | P 2 21 21 | a: 56.818 Å | b: 113.801 Å | c: 131.164 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 2.40 Å | Reflections | 33972 | Test set | 1931 (5.7%) | ||
R | 0.2117 | R-free | 0.2414 | ||||
According to PDB-REDO | |||||||
Resolution | 2.40 Å | Reflections | 33972 | Test set | 1682 (5.0%) 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) |
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Links | |||||||
PDBe | RCSB PDB | 3D bionotes | Proteopedia |
Original | PDB-REDO | |
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Crystallographic refinement | ||
R | 0.2805 | 0.1819 |
R-free | 0.2579 R-free was considered biased, the estimated unbiased R-free was used | 0.2160 |
Bond length RMS Z-score | 2.873 | 0.337 |
Bond angle RMS Z-score | 0.858 | 0.644 |
Model quality | ||
Ramachandran plot normality | -0.776 62 | -0.755 62 |
Rotamer normality | -2.008 51 | -1.205 68 |
Coarse packing | N/A N/A | N/A N/A |
Fine packing | N/A N/A | N/A N/A |
Bump severity | 0.000 95 | 0.000 95 |
Hydrogen bond satisfaction | N/A N/A | N/A N/A |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 11 |
Side chains flipped | 1 |
Waters removed | 35 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 48 |
Residues fitting density worse | 0 |