| Complex structure of MERS-CoV spike RBD bound to CD26 |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 2.2 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 61 2 2 | a: 110.224 Å | b: 110.224 Å | c: 527.599 Å | α: 90.00° | β: 90.00° | γ: 120.00° |
| Resolution | 2.70 Å | Reflections | 53442 | Test set | 2712 (5.1%) | ||
| R | 0.1982 | R-free | 0.2324 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.70 Å | Reflections | 53442 | Test set | 2712 (5.1%) | ||
| Twin | false | Radiation damage | 26 | ||||
| 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 | 0.2135 | 0.1869 |
| R-free | 0.2403 | 0.2266 |
| Bond length RMS Z-score | 0.592 | 0.392 |
| Bond angle RMS Z-score | 0.746 | 0.615 |
| Model quality | ||
| Ramachandran plot normality | -2.357 25 | -2.133 29 |
| Rotamer normality | -3.026 32 | -2.204 47 |
| Coarse packing | 0.181 57 | 0.152 56 |
| Fine packing | -1.356 38 | -1.347 38 |
| Bump severity | 0.532 1 | 0.472 2 |
| Hydrogen bond satisfaction | 0.849 13 | 0.853 15 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 16 |
| Side chains flipped | 0 |
| Waters removed | 28 |
| Peptides flipped | 2 |
| Chiralities fixed | 0 |
| Residues fitting density better | 19 |
| Residues fitting density worse | 0 |