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Crystal structure of spike protein receptor-binding domain from a predicted SARS coronavirus civet strain complexed with human-civet chimeric receptor ACE2 |
This entry was created with PDB-REDO version 7.32. |
From original header | |||||||
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Spacegroup | P 1 21 1 | a: 81.219 Å | b: 119.277 Å | c: 113.236 Å | α: 90.00° | β: 92.19° | γ: 90.00° |
Resolution | 3.00 Å | Reflections | 33732 | Test set | 1725 (5.1%) | ||
R | 0.2390 | R-free | 0.2850 | ||||
According to PDB-REDO | |||||||
Resolution | 2.99 Å | Reflections | 33732 | Test set | 1725 (5.1%) | ||
Twin | false | Radiation damage | N/A | ||||
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 | 0.2497 | 0.2492 |
R-free | 0.2954 | 0.2944 |
Bond length RMS Z-score | 0.503 | 0.378 |
Bond angle RMS Z-score | 0.640 | 0.677 |
Model quality | ||
Ramachandran plot normality | -7.317 1 | -4.770 6 |
Rotamer normality | -5.063 15 | -5.003 15 |
Coarse packing | -2.074 2 | -1.429 7 |
Fine packing | -2.670 4 | -2.106 12 |
Bump severity | 0.089 11 | 0.237 4 |
Hydrogen bond satisfaction | 0.794 5 | 0.802 5 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 41 |
Side chains flipped | 0 |
Waters removed | 0 |
Peptides flipped | 37 |
Chiralities fixed | 0 |
Residues fitting density better | 56 |
Residues fitting density worse | 7 |