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Structure of IMPa from Pseudomonas aeruginosa in complex with an O- glycopeptide |
This entry was created with PDB-REDO version 8.04. |
From original header | |||||||
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Spacegroup | P 1 21 1 | a: 90.340 Å | b: 156.500 Å | c: 95.680 Å | α: 90.00° | β: 114.31° | γ: 90.00° |
Resolution | 2.45 Å | Reflections | 88328 | Test set | 4347 (4.9%) | ||
R | 0.1799 | R-free | 0.2341 | ||||
According to PDB-REDO | |||||||
Resolution | 2.45 Å | Reflections | 88328 | Test set | 4375 (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 | 0.2088 | 0.2094 |
R-free | 0.2504 R-free was considered biased, the estimated unbiased R-free was used | 0.2411 |
Bond length RMS Z-score | 0.711 | 0.372 |
Bond angle RMS Z-score | 0.753 | 0.554 |
Model quality | ||
Ramachandran plot normality | -2.746 19 | -1.887 32 |
Rotamer normality | -3.530 32 | -1.365 70 |
Coarse packing | 0.636 87 | 0.666 87 |
Fine packing | -1.424 35 | -1.150 47 |
Bump severity | 0.008 64 | 0.015 47 |
Hydrogen bond satisfaction | 0.901 52 | 0.909 63 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 16 |
Side chains flipped | 4 |
Waters removed | 51 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 0 |