This entry is not up to date with the most recent version of PDB-REDO.
Please log in
to request an update.
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102340 |
This entry was created with PDB-REDO version 7.34. |
From original header | |||||||
---|---|---|---|---|---|---|---|
Spacegroup | C 1 2 1 | a: 112.875 Å | b: 53.127 Å | c: 44.387 Å | α: 90.00° | β: 103.04° | γ: 90.00° |
Resolution | 1.62 Å | Reflections | 32543 | Test set | 1618 (5.0%) | ||
R | 0.1820 | R-free | 0.2200 | ||||
According to PDB-REDO | |||||||
Resolution | 1.62 Å | Reflections | 32543 | Test set | 1618 (5.0%) | ||
Twin | false | Radiation damage | N/A | ||||
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 | 0.1888 | 0.1935 |
R-free | 0.2246 | 0.2233 |
Bond length RMS Z-score | 0.666 | 0.492 |
Bond angle RMS Z-score | 1.036 | 0.753 |
Model quality | ||
Ramachandran plot normality | -0.956 54 | -0.731 61 |
Rotamer normality | -0.793 81 | -0.441 87 |
Coarse packing | -0.254 49 | -0.262 48 |
Fine packing | -1.466 33 | -1.448 34 |
Bump severity | 0.005 74 | 0.009 61 |
Hydrogen bond satisfaction | 0.882 30 | 0.875 25 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 7 |
Side chains flipped | 0 |
Waters removed | 45 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 0 |