| Structure of MERS-Coronavirus Spike Receptor-binding Domain (England1 Strain) in Complex with Vaccine-Elicited Murine Neutralizing Antibody D12 (Crystal Form 2) |
| 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: 76.181 Å | b: 106.145 Å | c: 171.067 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
| Resolution | 3.20 Å | Reflections | 19380 | Test set | 942 (4.9%) | ||
| R | 0.2230 | R-free | 0.2812 | ||||
| According to PDB-REDO | |||||||
| Resolution | 3.20 Å | Reflections | 19380 | Test set | 942 (4.9%) | ||
| Twin | false | Radiation damage | N/A | ||||
| 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 | 0.2475 | 0.2277 |
| R-free | 0.2679 | 0.2648 |
| Bond length RMS Z-score | 1.935 | 0.263 |
| Bond angle RMS Z-score | 1.149 | 0.511 |
| Model quality | ||
| Ramachandran plot normality | 0.580 91 | -1.522 42 |
| Rotamer normality | -6.804 2 | -4.859 11 |
| Coarse packing | -0.472 28 | -0.189 40 |
| Fine packing | -1.109 49 | -0.330 76 |
| Bump severity | 1.344 0 | 0.149 7 |
| Hydrogen bond satisfaction | 0.799 5 | 0.855 15 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 18 |
| Side chains flipped | 3 |
| Waters removed | 0 |
| Peptides flipped | 12 |
| Chiralities fixed | 0 |
| Residues fitting density better | 10 |
| Residues fitting density worse | 0 |