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Crystal structure of spike protein receptor-binding domain from the 2005-2006 SARS coronavirus civet strain complexed with human-civet chimeric receptor ACE2 |
This entry was created with PDB-REDO version 7.31. |
From original header | |||||||
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Spacegroup | P 21 | a: 80.424 Å | b: 119.823 Å | c: 109.772 Å | α: 90.00° | β: 95.50° | γ: 90.00° |
Resolution | 2.90 Å | Reflections | 46190 | Test set | 0 (0.0%) | ||
R | 0.2240 | R-free | 0.2780 | ||||
According to PDB-REDO | |||||||
Resolution | 2.89 Å | Reflections | 46190 | Test set |
2227 (4.8%)
|
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 | |
---|---|---|
Crystallographic refinement | ||
R | 0.2499 | 0.2202 |
R-free |
0.3027
|
0.2569 |
Bond length RMS Z-score | 0.475 | 0.385 |
Bond angle RMS Z-score | 0.610 | 0.669 |
Model quality | ||
Ramachandran plot normality | -5.922 3 | -3.978 9 |
Rotamer normality | -4.778 17 | -3.565 31 |
Coarse packing | -1.410 8 | -0.931 18 |
Fine packing | -1.939 16 | -1.253 42 |
Bump severity | 0.032 28 | 0.092 11 |
Hydrogen bond satisfaction | 0.831 9 | 0.841 11 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 30 |
Side chains flipped | 0 |
Waters removed | 7 |
Peptides flipped | 21 |
Chiralities fixed | 0 |
Residues fitting density better | 36 |
Residues fitting density worse | 6 |