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Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with ACE2 |
This entry was created with PDB-REDO version 7.34. |
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 | 0.2270 | ||||
According to PDB-REDO | |||||||
Resolution | 2.45 Å | Reflections | 47591 | Test set | 2426 (5.1%) | Twin | false |
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 | 0.2096 | 0.2004 |
R-free | 0.2387 | 0.2376 |
Bond length RMS Z-score | 0.347 | 0.488 |
Bond angle RMS Z-score | 0.633 | 0.716 |
Model quality | ||
Ramachandran plot normality | -2.316 24 | -2.615 20 |
Rotamer normality | -2.844 42 | -2.652 46 |
Coarse packing | -0.382 42 | -0.493 36 |
Fine packing | -0.930 56 | -0.923 56 |
Bump severity | 0.304 3 | 0.325 3 |
Hydrogen bond satisfaction | 0.898 48 | 0.878 27 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 11 |
Side chains flipped | 0 |
Waters removed | 33 |
Peptides flipped | 5 |
Chiralities fixed | 0 |
Residues fitting density better | 14 |
Residues fitting density worse | 1 |