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PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z1741970824 |
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: 112.469 Å | b: 52.697 Å | c: 52.697 Å | α: 90.00° | β: 103.06° | γ: 90.00° |
Resolution | 1.50 Å | Reflections | 40023 | Test set | 1943 (4.9%) | ||
R | 0.1853 | R-free | 0.2210 | ||||
According to PDB-REDO | |||||||
Resolution | 1.50 Å | Reflections | 40023 | Test set | 1943 (4.9%) | ||
Twin | false | Radiation damage | 5 | ||||
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 | 0.2044 | 0.2030 |
R-free | 0.2402 | 0.2412 |
Bond length RMS Z-score | 1.274 | 0.342 |
Bond angle RMS Z-score | 0.969 | 0.572 |
Model quality | ||
Ramachandran plot normality | -0.850 60 | -0.686 64 |
Rotamer normality | -0.685 78 | 0.019 90 |
Coarse packing | 0.561 72 | 0.481 69 |
Fine packing | -1.579 28 | -1.461 33 |
Bump severity | 0.002 85 | 0.003 81 |
Hydrogen bond satisfaction | 0.872 23 | 0.887 35 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 6 |
Side chains flipped | 0 |
Waters removed | 30 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 0 |