PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102911 |
This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 1.5 |
From original header | |||||||
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Spacegroup | C 1 2 1 | a: 113.335 Å | b: 53.297 Å | c: 44.517 Å | α: 90.00° | β: 103.12° | γ: 90.00° |
Resolution | 1.96 Å | Reflections | 18577 | Test set | 965 (5.2%) | ||
R | 0.1958 | R-free | 0.2735 | ||||
According to PDB-REDO | |||||||
Resolution | 1.96 Å | Reflections | 18577 | Test set | 965 (5.2%) | ||
Twin | false | Radiation damage | 13 | ||||
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 | |
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Crystallographic refinement | ||
R | 0.2136 | 0.2168 |
R-free | 0.2707 | 0.2670 |
Bond length RMS Z-score | 1.298 | 0.167 |
Bond angle RMS Z-score | 0.937 | 0.422 |
Model quality | ||
Ramachandran plot normality | -1.330 46 | -0.706 64 |
Rotamer normality | -2.248 46 | -1.712 57 |
Coarse packing | 0.286 62 | 0.258 61 |
Fine packing | -0.536 70 | -0.592 68 |
Bump severity | 0.005 72 | 0.015 45 |
Hydrogen bond satisfaction | 0.859 17 | 0.852 14 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 7 |
Side chains flipped | 0 |
Waters removed | 67 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 0 |