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PanDDA analysis group deposition -- Crystal Structure of COVID-19 main protease in complex with Z1367324110 |
This entry was created with PDB-REDO version 8.07 using the deposited PDB model version 1.5 |
From original header | |||||||
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Spacegroup | C 1 2 1 | a: 113.780 Å | b: 53.490 Å | c: 53.490 Å | α: 90.00° | β: 101.70° | γ: 90.00° |
Resolution | 1.95 Å | Reflections | 19192 | Test set | 985 (5.1%) | ||
R | 0.1820 | R-free | 0.2494 | ||||
According to PDB-REDO | |||||||
Resolution | 1.95 Å | Reflections | 19192 | Test set | 985 (5.1%) | ||
Twin | false | Radiation damage | 39 | ||||
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 | 0.2078 | 0.2080 |
R-free | 0.2457 | 0.2499 |
Bond length RMS Z-score | 1.348 | 0.207 |
Bond angle RMS Z-score | 1.021 | 0.457 |
Model quality | ||
Ramachandran plot normality | -2.251 27 | -1.497 42 |
Rotamer normality | -2.713 37 | -1.266 66 |
Coarse packing | 0.334 64 | 0.300 62 |
Fine packing | -1.623 27 | -1.378 37 |
Bump severity | 0.009 59 | 0.004 76 |
Hydrogen bond satisfaction | 0.852 14 | 0.891 39 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 7 |
Side chains flipped | 0 |
Waters removed | 132 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 1 |
Residues fitting density worse | 0 |