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PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102578 |
This entry was created with PDB-REDO version 7.34. |
From original header | |||||||
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Spacegroup | C 1 2 1 | a: 112.394 Å | b: 52.591 Å | c: 44.385 Å | α: 90.00° | β: 103.04° | γ: 90.00° |
Resolution | 1.88 Å | Reflections | 20647 | Test set | 1051 (5.1%) | ||
R | 0.1680 | R-free | 0.2270 | ||||
According to PDB-REDO | |||||||
Resolution | 1.88 Å | Reflections | 20647 | Test set | 1051 (5.1%) | Twin | false |
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 | 0.1742 | 0.2114 |
R-free | 0.2297 | 0.2609 |
Bond length RMS Z-score | 0.648 | 0.574 |
Bond angle RMS Z-score | 1.033 | 0.808 |
Model quality | ||
Ramachandran plot normality | -1.407 42 | -2.341 24 |
Rotamer normality | -0.986 78 | -1.346 71 |
Coarse packing | -0.096 57 | -0.218 50 |
Fine packing | -1.373 37 | -1.356 38 |
Bump severity | 0.005 74 | 0.008 64 |
Hydrogen bond satisfaction | 0.906 58 | 0.890 38 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 9 |
Side chains flipped | 0 |
Waters removed | 61 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 2 |