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SARS-COV-2 OMICRON BA.4/5 RBD IN COMPLEX WITH BETA-27 FAB AND C1 NANOBODY |
This entry was created with PDB-REDO version 7.38. |
From original header | |||||||
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Spacegroup | P 21 21 21 | a: 84.105 Å | b: 100.436 Å | c: 105.443 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 1.89 Å | Reflections | 72006 | Test set | 3760 (5.2%) | ||
R | 0.1810 | R-free | 0.2090 | ||||
According to PDB-REDO | |||||||
Resolution | 1.89 Å | Reflections | 72006 | Test set | 3755 (5.2%) 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 | |
---|---|---|
Crystallographic refinement | ||
R | 0.1901 | 0.1833 |
R-free | 0.2236 R-free was considered biased, the estimated unbiased R-free was used | 0.2159 |
Bond length RMS Z-score | 0.185 | 0.567 |
Bond angle RMS Z-score | 0.517 | 0.778 |
Model quality | ||
Ramachandran plot normality | 0.349 87 | -0.668 63 |
Rotamer normality | 0.384 95 | -1.065 76 |
Coarse packing | 0.071 65 | 0.052 65 |
Fine packing | -0.277 77 | -0.249 77 |
Bump severity | 0.064 15 | 0.062 16 |
Hydrogen bond satisfaction | 0.894 43 | 0.899 49 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 11 |
Side chains flipped | 2 |
Waters removed | 76 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 14 |
Residues fitting density worse | 0 |