| Crystal structure of SARS spike protein receptor binding domain in complex with a neutralizing antibody, 80R |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 1.4 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 1 21 1 | a: 47.453 Å | b: 175.902 Å | c: 67.561 Å | α: 90.00° | β: 96.55° | γ: 90.00° |
| Resolution | 2.30 Å | Reflections | 51859 | Test set | 2617 (5.0%) | ||
| R | 0.2484 | R-free | 0.2954 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.19 Å | Reflections | 51859 | Test set |
2616 (5.0%)
New test set, PDB-REDO compensated for this
|
||
| Twin | false | Radiation damage | 46 | ||||
| PDB-REDO files | |||||||
| Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
|||||
| Links | |||||||
| PDBe | RCSB PDB | 3D bionotes | Proteopedia | ||||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.2853 | 0.2412 |
| R-free |
0.3418
R-free was considered biased, the
estimated unbiased R-free was used
|
0.2833 |
| Bond length RMS Z-score | 0.713 | 0.202 |
| Bond angle RMS Z-score | 0.667 | 0.446 |
| Model quality | ||
| Ramachandran plot normality | -1.790 35 | -1.671 38 |
| Rotamer normality | -2.382 43 | -0.719 78 |
| Coarse packing | -0.023 48 | -0.023 48 |
| Fine packing | 0.657 92 | 0.780 93 |
| Bump severity | 0.007 65 | 0.006 68 |
| Hydrogen bond satisfaction | 0.864 19 | 0.868 21 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 16 |
| Side chains flipped | 0 |
| Waters removed | 19 |
| Peptides flipped | 4 |
| Chiralities fixed | 0 |
| Residues fitting density better | 11 |
| Residues fitting density worse | 0 |