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PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z3241250482 |
This entry was created with PDB-REDO version 8.07. |
From original header | |||||||
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Spacegroup | C 1 2 1 | a: 112.225 Å | b: 52.701 Å | c: 52.701 Å | α: 90.00° | β: 102.89° | γ: 90.00° |
Resolution | 1.74 Å | Reflections | 26161 | Test set | 1302 (5.0%) | ||
R | 0.1776 | R-free | 0.2306 | ||||
According to PDB-REDO | |||||||
Resolution | 1.74 Å | Reflections | 26161 | Test set | 1302 (5.0%) | ||
Twin | false | Radiation damage | 3 | ||||
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 | 0.1867 | 0.1932 |
R-free | 0.2370 | 0.2404 |
Bond length RMS Z-score | 1.304 | 0.448 |
Bond angle RMS Z-score | 0.982 | 0.619 |
Model quality | ||
Ramachandran plot normality | -1.466 43 | -1.102 53 |
Rotamer normality | -0.997 72 | -0.110 88 |
Coarse packing | 0.524 71 | 0.431 68 |
Fine packing | -1.636 26 | -1.453 34 |
Bump severity | 0.003 81 | 0.004 76 |
Hydrogen bond satisfaction | 0.905 57 | 0.897 46 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 6 |
Side chains flipped | 0 |
Waters removed | 63 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 0 |