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| Structure of the N-terminal domain (NTD)of SARS-CoV spike protein |
| This entry was created with PDB-REDO version 7.32. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 61 2 2 | a: 73.291 Å | b: 73.291 Å | c: 240.263 Å | α: 90.00° | β: 90.00° | γ: 120.00° |
| Resolution | 2.20 Å | Reflections | 20247 | Test set | 1040 (5.1%) | ||
| R | 0.2520 | R-free | 0.2820 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.20 Å | Reflections | 20247 | Test set | 1040 (5.1%) | ||
| 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 | 0.2599 | 0.2287 |
| R-free | 0.2850 | 0.2734 |
| Bond length RMS Z-score | 0.228 | 0.717 |
| Bond angle RMS Z-score | 0.556 | 0.890 |
| Model quality | ||
| Ramachandran plot normality | -3.006 16 | -2.348 24 |
| Rotamer normality | -2.288 52 | -2.962 40 |
| Coarse packing | -0.619 30 | -0.529 35 |
| Fine packing | -1.834 19 | -1.626 26 |
| Bump severity | 0.447 2 | 0.711 1 |
| Hydrogen bond satisfaction | 0.860 17 | 0.888 36 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 3 |
| Side chains flipped | 0 |
| Waters removed | 12 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 10 |
| Residues fitting density worse | 0 |