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The crystal structure of COVID-19 main protease in complex with an inhibitor N3 |
This entry was created with PDB-REDO version 8.04. |
From original header | |||||||
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Spacegroup | C 1 2 1 | a: 97.931 Å | b: 79.477 Å | c: 51.803 Å | α: 90.00° | β: 114.55° | γ: 90.00° |
Resolution | 2.16 Å | Reflections | 19454 | Test set | 998 (5.1%) | ||
R | 0.2020 | R-free | 0.2350 | ||||
According to PDB-REDO | |||||||
Resolution | 2.16 Å | Reflections | 19454 | Test set | 998 (5.1%) | ||
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 | |
---|---|---|
Crystallographic refinement | ||
R | 0.2184 | 0.1819 |
R-free | 0.2499 | 0.2234 |
Bond length RMS Z-score | 0.824 | 0.309 |
Bond angle RMS Z-score | 0.782 | 0.629 |
Model quality | ||
Ramachandran plot normality | -1.937 32 | -1.561 41 |
Rotamer normality | -2.641 38 | -0.930 73 |
Coarse packing | N/A N/A | N/A N/A |
Fine packing | N/A N/A | N/A N/A |
Bump severity | 5.234 0 | 0.000 95 |
Hydrogen bond satisfaction | N/A N/A | N/A N/A |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 8 |
Side chains flipped | 0 |
Waters removed | 15 |
Peptides flipped | 1 |
Chiralities fixed | 9 |
Residues fitting density better | 14 |
Residues fitting density worse | 0 |