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PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102539 |
This entry was created with PDB-REDO version 7.34. |
From original header | |||||||
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Spacegroup | C 1 2 1 | a: 113.529 Å | b: 53.304 Å | c: 44.465 Å | α: 90.00° | β: 103.23° | γ: 90.00° |
Resolution | 2.06 Å | Reflections | 16048 | Test set | 821 (5.1%) | ||
R | 0.1780 | R-free | 0.2570 | ||||
According to PDB-REDO | |||||||
Resolution | 2.06 Å | Reflections | 16048 | Test set | 821 (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 | 0.1858 | 0.2052 |
R-free | 0.2655 | 0.2630 |
Bond length RMS Z-score | 0.699 | 0.387 |
Bond angle RMS Z-score | 1.059 | 0.654 |
Model quality | ||
Ramachandran plot normality | -2.043 29 | -1.568 38 |
Rotamer normality | -2.353 51 | -1.241 73 |
Coarse packing | -0.434 39 | -0.428 40 |
Fine packing | -1.655 25 | -1.560 29 |
Bump severity | 0.008 64 | 0.003 82 |
Hydrogen bond satisfaction | 0.875 25 | 0.891 39 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 10 |
Side chains flipped | 0 |
Waters removed | 68 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 0 |