| Structure of the N-terminal domain (NTD) of MERS-CoV spike protein |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 2.1 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 21 21 21 | a: 51.615 Å | b: 86.609 Å | c: 88.098 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
| Resolution | 1.50 Å | Reflections | 60852 | Test set | 3080 (5.1%) | ||
| R | 0.1625 | R-free | 0.1946 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.50 Å | Reflections | 60852 | Test set | 3080 (5.1%) | ||
| Twin | false | Radiation damage | 3 | ||||
| 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 | 0.1675 | 0.1883 |
| R-free | 0.1964 | 0.2073 |
| Bond length RMS Z-score | 0.512 | 0.569 |
| Bond angle RMS Z-score | 0.606 | 0.685 |
| Model quality | ||
| Ramachandran plot normality | -0.968 56 | -1.070 53 |
| Rotamer normality | 0.222 92 | 0.225 92 |
| Coarse packing | -0.106 44 | -0.104 44 |
| Fine packing | -0.929 56 | -1.125 48 |
| Bump severity | 0.379 2 | 0.389 2 |
| Hydrogen bond satisfaction | 0.829 9 | 0.836 10 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 4 |
| Side chains flipped | 0 |
| Waters removed | 3 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 2 |