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Human cathepsin-C in complex with dipeptidyl cyclopropyl nitrile inhibitor 3 |
This entry was created with PDB-REDO version 7.32. |
From original header | |||||||
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Spacegroup | I 2 2 2 | a: 87.365 Å | b: 87.549 Å | c: 115.004 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 2.00 Å | Reflections | 32143 | Test set | 1750 (5.4%) | ||
R | 0.1600 | R-free | 0.2030 | ||||
According to PDB-REDO | |||||||
Resolution | 1.92 Å | Reflections | 32143 | Test set | 1595 (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 | 0.2552 | 0.1657 |
R-free | 0.3017 R-free was considered biased, the estimated unbiased R-free was used | 0.2041 |
Bond length RMS Z-score | 0.825 | 0.549 |
Bond angle RMS Z-score | 1.091 | 0.749 |
Model quality | ||
Ramachandran plot normality | -1.606 38 | -1.509 40 |
Rotamer normality | -1.531 67 | -0.767 81 |
Coarse packing | -0.597 32 | -0.579 32 |
Fine packing | -1.414 35 | -1.412 35 |
Bump severity | 0.423 2 | 0.491 2 |
Hydrogen bond satisfaction | 0.899 49 | 0.900 50 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 4 |
Side chains flipped | 0 |
Waters removed | 21 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 0 |