Structural and spectroscopic analysis of the kinase inhibitor bosutinib binding to the Abl tyrosine kinase domain |
This entry was created with PDB-REDO version 8.08. |
From original header | |||||||
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Spacegroup | P 2 21 21 | a: 56.860 Å | b: 113.760 Å | c: 127.640 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 2.42 Å | Reflections | 30134 | Test set | 2052 (6.8%) | ||
R | 0.1880 | R-free | 0.2487 | ||||
According to PDB-REDO | |||||||
Resolution | 2.42 Å | Reflections | 30134 | Test set | 2028 (6.7%) New test set, PDB-REDO compensated for this | ||
Twin | false | Radiation damage | 79 | ||||
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 | 0.1901 | 0.1925 |
R-free | 0.2277 R-free was considered biased, the estimated unbiased R-free was used | 0.2306 |
Bond length RMS Z-score | 1.105 | 0.226 |
Bond angle RMS Z-score | 0.715 | 0.467 |
Model quality | ||
Ramachandran plot normality | -1.972 32 | -0.609 66 |
Rotamer normality | -3.378 26 | -1.038 71 |
Coarse packing | 0.571 73 | 0.516 71 |
Fine packing | -0.107 81 | 0.227 87 |
Bump severity | 0.007 65 | 0.005 72 |
Hydrogen bond satisfaction | 0.885 33 | 0.734 2 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
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Rotamers changed | 8 |
Side chains flipped | 2 |
Waters removed | 4 |
Peptides flipped | 3 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 3 |