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 8.13 using the deposited PDB model version 1.5 |
From original header | |||||||
---|---|---|---|---|---|---|---|
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 | 0.1779 | R-free | 0.2572 | ||||
According to PDB-REDO | |||||||
Resolution | 2.06 Å | Reflections | 16048 | Test set | 821 (5.1%) | ||
Twin | false | Radiation damage | 22 | ||||
PDB-REDO files | |||||||
Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
|||||
Links | |||||||
PDBe | RCSB PDB | 3D bionotes | Proteopedia |
Original | PDB-REDO | |
---|---|---|
Crystallographic refinement | ||
R | 0.1862 | 0.1996 |
R-free | 0.2662 | 0.2618 |
Bond length RMS Z-score | 1.347 | 0.168 |
Bond angle RMS Z-score | 1.020 | 0.405 |
Model quality | ||
Ramachandran plot normality | -1.886 33 | -1.268 48 |
Rotamer normality | -2.354 44 | -0.362 84 |
Coarse packing | 0.303 63 | 0.193 58 |
Fine packing | -0.746 63 | -0.714 64 |
Bump severity | 0.003 81 | 0.003 81 |
Hydrogen bond satisfaction | 0.860 17 | 0.863 18 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 7 |
Side chains flipped | 0 |
Waters removed | 66 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 0 |