| Structure of the N-terminal domain (NTD)of SARS-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 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 | 0.2519 | R-free | 0.2824 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.20 Å | Reflections | 20247 | Test set | 1040 (5.1%) | ||
| Twin | false | Radiation damage | 86 | ||||
| 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 | 0.2607 | 0.2235 |
| R-free | 0.2857 | 0.2596 |
| Bond length RMS Z-score | 0.492 | 0.751 |
| Bond angle RMS Z-score | 0.641 | 0.781 |
| Model quality | ||
| Ramachandran plot normality | -2.979 17 | -2.402 24 |
| Rotamer normality | -2.288 45 | -2.233 46 |
| Coarse packing | -0.619 23 | -0.450 29 |
| Fine packing | -1.466 33 | -1.201 45 |
| Bump severity | 0.447 2 | 0.520 1 |
| Hydrogen bond satisfaction | 0.806 6 | 0.816 7 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 1 |
| Side chains flipped | 0 |
| Waters removed | 13 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 13 |
| Residues fitting density worse | 0 |