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PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z126932614 |
This entry was created with PDB-REDO version 8.07. |
From original header | |||||||
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Spacegroup | C 1 2 1 | a: 111.952 Å | b: 52.630 Å | c: 52.630 Å | α: 90.00° | β: 102.98° | γ: 90.00° |
Resolution | 1.41 Å | Reflections | 45835 | Test set | 2211 (4.8%) | ||
R | 0.1776 | R-free | 0.2110 | ||||
According to PDB-REDO | |||||||
Resolution | 1.41 Å | Reflections | 45835 | Test set | 2211 (4.8%) | ||
Twin | false | Radiation damage | 30 | ||||
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 | 0.1857 | 0.1859 |
R-free | 0.2175 | 0.2166 |
Bond length RMS Z-score | 1.302 | 0.414 |
Bond angle RMS Z-score | 1.004 | 0.614 |
Model quality | ||
Ramachandran plot normality | -0.370 73 | -0.342 74 |
Rotamer normality | 0.035 90 | 0.668 96 |
Coarse packing | 0.516 71 | 0.484 70 |
Fine packing | -1.530 30 | -1.441 34 |
Bump severity | 0.006 68 | 0.005 72 |
Hydrogen bond satisfaction | 0.889 37 | 0.894 42 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 3 |
Side chains flipped | 0 |
Waters removed | 42 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 1 |