| Structure of MERS-Coronavirus Spike Receptor-binding Domain (England1 Strain) in Complex with Vaccine-Elicited Murine Neutralizing Antibody D12 (Crystal Form 1) |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 1.2 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 21 21 21 | a: 74.452 Å | b: 128.790 Å | c: 170.871 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
| Resolution | 2.59 Å | Reflections | 51227 | Test set | 2529 (4.9%) | ||
| R | 0.2038 | R-free | 0.2441 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.59 Å | Reflections | 51227 | Test set | 2529 (4.9%) | ||
| Twin | false | Radiation damage | 89 | ||||
| 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 | 0.2228 | 0.1964 |
| R-free | 0.2518 | 0.2406 |
| Bond length RMS Z-score | 1.121 | 0.249 |
| Bond angle RMS Z-score | 0.853 | 0.487 |
| Model quality | ||
| Ramachandran plot normality | -0.039 81 | -0.477 70 |
| Rotamer normality | -2.305 45 | -1.100 70 |
| Coarse packing | 0.399 66 | 0.511 71 |
| Fine packing | 0.578 91 | 0.768 93 |
| Bump severity | 0.153 7 | 0.083 11 |
| Hydrogen bond satisfaction | 0.883 31 | 0.731 2 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 18 |
| Side chains flipped | 0 |
| Waters removed | 28 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 10 |
| Residues fitting density worse | 0 |