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| Crystal structure of RNA binding domain of nucleocapsid phosphoprotein from SARS coronavirus 2 |
| This entry was created with PDB-REDO version 8.08 using the deposited PDB model version 3.2 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 21 21 21 | a: 66.238 Å | b: 77.430 Å | c: 114.039 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
| Resolution | 1.70 Å | Reflections | 56892 | Test set | 2802 (4.9%) | ||
| R | 0.1592 | R-free | 0.2053 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.70 Å | Reflections | 56892 | Test set | 2802 (4.9%) | ||
| Twin | false | Radiation damage | 82 | ||||
| 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 | 0.1688 | 0.1702 |
| R-free | 0.2075 | 0.2024 |
| Bond length RMS Z-score | 0.654 | 0.886 |
| Bond angle RMS Z-score | 0.700 | 0.885 |
| Model quality | ||
| Ramachandran plot normality | 1.794 98 | 1.496 97 |
| Rotamer normality | 1.058 98 | 0.565 95 |
| Coarse packing | -2.257 1 | -2.275 1 |
| Fine packing | -1.379 37 | -1.419 35 |
| Bump severity | 0.064 14 | 0.062 15 |
| Hydrogen bond satisfaction | 0.924 81 | 0.908 61 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 7 |
| Side chains flipped | 0 |
| Waters removed | 53 |
| Peptides flipped | 1 |
| Chiralities fixed | 0 |
| Residues fitting density better | 3 |
| Residues fitting density worse | 1 |