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Structure of SARS-CoV-2 chimeric receptor-binding domain complexed with its receptor human ACE2 |
This entry was created with PDB-REDO version 8.04. |
From original header | |||||||
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Spacegroup | P 1 21 1 | a: 80.435 Å | b: 118.034 Å | c: 112.075 Å | α: 90.00° | β: 93.12° | γ: 90.00° |
Resolution | 2.68 Å | Reflections | 58223 | Test set | 2675 (4.6%) | ||
R | 0.1970 | R-free | 0.2288 | ||||
According to PDB-REDO | |||||||
Resolution | 2.68 Å | Reflections | 58223 | Test set | 2675 (4.6%) | ||
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 | 0.2124 | 0.1970 |
R-free | 0.2371 | 0.2368 |
Bond length RMS Z-score | 0.535 | 0.384 |
Bond angle RMS Z-score | 0.660 | 0.602 |
Model quality | ||
Ramachandran plot normality | -1.844 33 | -3.374 13 |
Rotamer normality | -2.661 45 | -3.362 34 |
Coarse packing | 0.730 89 | 0.703 88 |
Fine packing | -1.152 47 | -1.389 36 |
Bump severity | 0.485 2 | 0.140 8 |
Hydrogen bond satisfaction | 0.861 17 | 0.802 5 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 26 |
Side chains flipped | 2 |
Waters removed | 9 |
Peptides flipped | 11 |
Chiralities fixed | 0 |
Residues fitting density better | 50 |
Residues fitting density worse | 4 |