Crystal structure of spike protein receptor-binding domain from the 2002-2003 SARS coronavirus civet strain complexed with human-civet chimeric receptor ACE2 |
This entry was created with PDB-REDO version 8.12 using the deposited PDB model version 2.1 |
From original header | |||||||
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Spacegroup | P 1 21 1 | a: 80.352 Å | b: 119.841 Å | c: 109.420 Å | α: 90.00° | β: 95.88° | γ: 90.00° |
Resolution | 3.10 Å | Reflections | 38250 | Test set | 0 (0.0%) | ||
R | 0.2210 | R-free | 0.3020 | ||||
According to PDB-REDO | |||||||
Resolution | 3.05 Å | Reflections | 38250 | Test set | 1896 (5.0%) New test set, PDB-REDO compensated for this | ||
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 | |
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Crystallographic refinement | ||
R | 0.2445 | 0.2342 |
R-free | 0.2861 R-free was considered biased, the estimated unbiased R-free was used | 0.2721 |
Bond length RMS Z-score | 0.781 | 0.374 |
Bond angle RMS Z-score | 0.748 | 0.600 |
Model quality | ||
Ramachandran plot normality | -6.401 2 | -5.043 4 |
Rotamer normality | -5.557 6 | -4.437 14 |
Coarse packing | 0.085 53 | 0.306 63 |
Fine packing | -2.179 10 | -1.702 23 |
Bump severity | 0.028 29 | 0.040 21 |
Hydrogen bond satisfaction | 0.812 7 | 0.821 8 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 43 |
Side chains flipped | 0 |
Waters removed | 7 |
Peptides flipped | 32 |
Chiralities fixed | 0 |
Residues fitting density better | 12 |
Residues fitting density worse | 3 |