Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with ACE2 |
This entry was created with PDB-REDO version 8.12. |
From original header | |||||||
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Spacegroup | P 41 21 2 | a: 104.670 Å | b: 104.670 Å | c: 228.720 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 2.45 Å | Reflections | 47591 | Test set | 2426 (5.1%) | ||
R | 0.1920 | R-free | 0.2269 | ||||
According to PDB-REDO | |||||||
Resolution | 2.45 Å | Reflections | 47591 | Test set | 2426 (5.1%) | ||
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 | 0.2106 | 0.1982 |
R-free | 0.2390 | 0.2381 |
Bond length RMS Z-score | 0.908 | 0.445 |
Bond angle RMS Z-score | 0.776 | 0.621 |
Model quality | ||
Ramachandran plot normality | -2.155 28 | -2.040 30 |
Rotamer normality | -2.844 35 | -2.524 40 |
Coarse packing | 1.037 86 | 0.989 85 |
Fine packing | -0.894 57 | -0.870 58 |
Bump severity | 0.304 3 | 0.308 3 |
Hydrogen bond satisfaction | 0.875 25 | 0.875 25 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 11 |
Side chains flipped | 0 |
Waters removed | 38 |
Peptides flipped | 3 |
Chiralities fixed | 0 |
Residues fitting density better | 19 |
Residues fitting density worse | 0 |