| structure of the receptor binding domain (RBD) of MERS-CoV spike |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 1.4 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 21 21 21 | a: 46.977 Å | b: 108.473 Å | c: 125.925 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
| Resolution | 2.51 Å | Reflections | 22483 | Test set | 1154 (5.1%) | ||
| R | 0.2079 | R-free | 0.2509 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.51 Å | Reflections | 22483 | Test set | 1154 (5.1%) | ||
| Twin | false | Radiation damage | 88 | ||||
| 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 | 0.2115 | 0.1893 |
| R-free | 0.2543 | 0.2301 |
| Bond length RMS Z-score | 0.543 | 0.441 |
| Bond angle RMS Z-score | 0.847 | 0.635 |
| Model quality | ||
| Ramachandran plot normality | -2.145 29 | -0.901 58 |
| Rotamer normality | -3.159 30 | -2.128 48 |
| Coarse packing | -0.447 29 | -0.202 39 |
| Fine packing | -1.948 16 | -1.758 21 |
| Bump severity | 0.272 4 | 0.235 4 |
| Hydrogen bond satisfaction | 0.828 9 | 0.830 9 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 14 |
| Side chains flipped | 0 |
| Waters removed | 13 |
| Peptides flipped | 3 |
| Chiralities fixed | 0 |
| Residues fitting density better | 12 |
| Residues fitting density worse | 0 |