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Structure of COVID-19 main protease bound to potent broad-spectrum non-covalent inhibitor X77 |
This entry was created with PDB-REDO version 7.29. |
From original header | |||||||
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Spacegroup | P 21 21 2 | a: 45.050 Å | b: 63.840 Å | c: 106.588 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 2.10 Å | Reflections | 18524 | Test set | 1852 (10%) | ||
R | 0.1500 | R-free | 0.2210 | ||||
According to PDB-REDO | |||||||
Resolution | 2.10 Å | Reflections | 18524 | Test set | 1869 (10.1%) 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) |
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Links | |||||||
PDBe | RCSB PDB | 3D bionotes | Proteopedia |
Original | PDB-REDO | |
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Crystallographic refinement | ||
R | 0.1597 | 0.1697 |
R-free | 0.2083 R-free was considered biased, the estimated unbiased R-free was used | 0.2403 |
Bond length RMS Z-score | 0.437 | 0.501 |
Bond angle RMS Z-score | 0.724 | 0.727 |
Model quality | ||
Ramachandran plot normality | -0.323 72 | -0.700 62 |
Rotamer normality | -2.238 53 | -2.069 57 |
Coarse packing | -0.544 34 | -0.585 32 |
Fine packing | -1.518 31 | -1.323 39 |
Bump severity | 0.010 58 | 0.002 87 |
Hydrogen bond satisfaction | 0.895 44 | 0.899 49 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 10 |
Side chains flipped | 0 |
Waters removed | 34 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 0 |