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Structure of SARS coronavirus spike receptor-binding domain complexed with its receptor |
This entry was created with PDB-REDO version 8.01. |
From original header | |||||||
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Spacegroup | P 1 21 1 | a: 82.299 Å | b: 119.429 Å | c: 113.237 Å | α: 90.00° | β: 91.97° | γ: 90.00° |
Resolution | 2.90 Å | Reflections | 46095 | Test set | 2254 (4.9%) | ||
R | 0.2180 | R-free | 0.2750 | ||||
According to PDB-REDO | |||||||
Resolution | 2.81 Å | Reflections | 46095 | Test set | 2254 (4.9%) | ||
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 | 0.2393 | 0.2217 |
R-free | 0.2954 | 0.2546 |
Bond length RMS Z-score | 0.413 | 0.445 |
Bond angle RMS Z-score | 0.618 | 0.751 |
Model quality | ||
Ramachandran plot normality | -5.919 3 | -4.367 7 |
Rotamer normality | -5.652 10 | -4.343 22 |
Coarse packing | -0.072 58 | 0.289 75 |
Fine packing | -2.401 7 | -1.674 25 |
Bump severity | 0.326 3 | 0.233 5 |
Hydrogen bond satisfaction | 0.814 6 | 0.801 5 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 39 |
Side chains flipped | 0 |
Waters removed | 27 |
Peptides flipped | 28 |
Chiralities fixed | 0 |
Residues fitting density better | 81 |
Residues fitting density worse | 2 |