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| Crystal structure of SARS-CoV-2 nucleocapsid protein N-terminal RNA binding domain |
| This entry was created with PDB-REDO version 8.04 using the deposited PDB model version 1.5 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 21 21 21 | a: 58.888 Å | b: 92.685 Å | c: 97.325 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
| Resolution | 2.70 Å | Reflections | 15125 | Test set | 1516 (10.0%) | ||
| R | 0.2578 | R-free | 0.2934 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.70 Å | Reflections | 15125 | Test set |
1514 (10.0%)
New test set, PDB-REDO compensated for this
|
||
| Twin | false | Radiation damage | N/A | ||||
| PDB-REDO files | |||||||
| Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
|||||
| Links | |||||||
| PDBe | RCSB PDB | 3D bionotes | Proteopedia | ||||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.2637 | 0.2413 |
| R-free |
0.3194
R-free was considered biased, the
estimated unbiased R-free was used
|
0.2850 |
| Bond length RMS Z-score | 0.544 | 0.410 |
| Bond angle RMS Z-score | 0.625 | 0.590 |
| Model quality | ||
| Ramachandran plot normality | -1.414 42 | -0.224 75 |
| Rotamer normality | -4.734 18 | -2.059 57 |
| Coarse packing | -2.965 1 | -2.691 1 |
| Fine packing | -1.779 21 | -0.560 69 |
| Bump severity | 0.036 25 | 0.037 24 |
| Hydrogen bond satisfaction | 0.860 17 | 0.869 21 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 5 |
| Side chains flipped | 20 |
| Waters removed | 8 |
| Peptides flipped | 3 |
| Chiralities fixed | 0 |
| Residues fitting density better | 1 |
| Residues fitting density worse | 0 |