| Structural definition of a unique neutralization epitope on the receptor-binding domain of MERS-CoV spike glycoprotein |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 1.2 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | H 3 | a: 138.647 Å | b: 138.647 Å | c: 228.736 Å | α: 90.00° | β: 90.00° | γ: 120.00° |
| Resolution | 4.48 Å | Reflections | 9479 | Test set | 0 (0.0%) | ||
| R | 0.3072 | R-free | 0.3430 | ||||
| According to PDB-REDO | |||||||
| Resolution | 4.48 Å | Reflections | 9479 | Test set |
962 (10.1%)
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) |
|||||
| Links | |||||||
| PDBe | RCSB PDB | 3D bionotes | Proteopedia | ||||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.3328 | 0.3306 |
| R-free |
0.3894
R-free was considered biased, the
estimated unbiased R-free was used
|
0.3637 |
| Bond length RMS Z-score | 0.561 | 0.472 |
| Bond angle RMS Z-score | 0.725 | 0.655 |
| Model quality | ||
| Ramachandran plot normality | -1.386 45 | -1.958 32 |
| Rotamer normality | -1.856 54 | -3.042 32 |
| Coarse packing | -0.367 32 | -0.499 27 |
| Fine packing | -0.989 54 | -1.029 52 |
| Bump severity | 0.062 15 | 0.035 24 |
| Hydrogen bond satisfaction | 0.840 11 | 0.828 9 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 8 |
| Side chains flipped | 0 |
| Waters removed | 0 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 92 |
| Residues fitting density worse | 1 |