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PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102535 |
This entry was created with PDB-REDO version 7.34. |
From original header | |||||||
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Spacegroup | C 1 2 1 | a: 112.645 Å | b: 52.876 Å | c: 44.444 Å | α: 90.00° | β: 103.13° | γ: 90.00° |
Resolution | 1.72 Å | Reflections | 26578 | Test set | 1317 (5.0%) | ||
R | 0.1880 | R-free | 0.2360 | ||||
According to PDB-REDO | |||||||
Resolution | 1.72 Å | Reflections | 26578 | Test set | 1317 (5.0%) | 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 | 0.1948 | 0.1955 |
R-free | 0.2382 | 0.2398 |
Bond length RMS Z-score | 0.640 | 0.372 |
Bond angle RMS Z-score | 1.025 | 0.660 |
Model quality | ||
Ramachandran plot normality | -1.997 30 | -1.622 37 |
Rotamer normality | -1.411 70 | -0.459 86 |
Coarse packing | -0.267 48 | -0.262 48 |
Fine packing | -1.544 30 | -1.466 33 |
Bump severity | 0.010 58 | 0.013 51 |
Hydrogen bond satisfaction | 0.887 35 | 0.881 29 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 8 |
Side chains flipped | 0 |
Waters removed | 63 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 0 |