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SARS-CoV-2 main protease with unliganded active site (2019-nCoV, coronavirus disease 2019, COVID-19) |
This entry was created with PDB-REDO version 8.08. |
From original header | |||||||
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Spacegroup | C 1 2 1 | a: 112.812 Å | b: 52.949 Å | c: 44.631 Å | α: 90.00° | β: 103.16° | γ: 90.00° |
Resolution | 1.39 Å | Reflections | 50331 | Test set | 2585 (5.1%) | ||
R | 0.1779 | R-free | 0.2000 | ||||
According to PDB-REDO | |||||||
Resolution | 1.39 Å | Reflections | 50331 | Test set | 2585 (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 | 0.1805 | 0.1362 |
R-free | 0.2306 R-free was considered biased, the estimated unbiased R-free was used | 0.1727 |
Bond length RMS Z-score | 0.744 | 0.945 |
Bond angle RMS Z-score | 0.747 | 0.899 |
Model quality | ||
Ramachandran plot normality | -0.279 76 | -0.757 62 |
Rotamer normality | 0.039 90 | 0.733 96 |
Coarse packing | 0.350 64 | 0.443 68 |
Fine packing | -1.711 23 | -1.584 28 |
Bump severity | 0.001 90 | 0.004 76 |
Hydrogen bond satisfaction | 0.890 38 | 0.891 39 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 4 |
Side chains flipped | 0 |
Waters removed | 62 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 199 |
Residues fitting density worse | 0 |