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PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102254 |
This entry was created with PDB-REDO version 7.34. |
From original header | |||||||
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Spacegroup | C 1 2 1 | a: 111.803 Å | b: 52.599 Å | c: 44.686 Å | α: 90.00° | β: 102.94° | γ: 90.00° |
Resolution | 1.55 Å | Reflections | 36472 | Test set | 1793 (4.9%) | ||
R | 0.1840 | R-free | 0.2160 | ||||
According to PDB-REDO | |||||||
Resolution | 1.55 Å | Reflections | 36472 | Test set | 1793 (4.9%) | 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 | 0.1919 | 0.2149 |
R-free | 0.2225 | 0.2457 |
Bond length RMS Z-score | 0.639 | 0.645 |
Bond angle RMS Z-score | 0.995 | 0.843 |
Model quality | ||
Ramachandran plot normality | -1.243 46 | -1.431 42 |
Rotamer normality | -0.887 79 | -0.971 78 |
Coarse packing | -0.232 50 | -0.294 47 |
Fine packing | -1.531 30 | -1.469 33 |
Bump severity | 0.006 70 | 0.015 47 |
Hydrogen bond satisfaction | 0.887 35 | 0.891 39 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 10 |
Side chains flipped | 0 |
Waters removed | 29 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 1 |