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| The 1.9 A Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with a Citrate |
| This entry was created with PDB-REDO version 7.31 using the deposited PDB model |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 63 | a: 150.784 Å | b: 150.784 Å | c: 111.682 Å | α: 90.00° | β: 90.00° | γ: 120.00° |
| Resolution | 1.90 Å | Reflections | 111315 | Test set | 5485 (4.9%) | ||
| R | 0.1610 | R-free | 0.1850 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.90 Å | Reflections | 111315 | Test set | 5485 (4.9%) | ||
| 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 | 0.1675 | 0.1590 |
| R-free | 0.1875 | 0.1839 |
| Bond length RMS Z-score | 0.458 | 0.532 |
| Bond angle RMS Z-score | 0.664 | 0.691 |
| Model quality | ||
| Ramachandran plot normality | -0.991 53 | -0.717 61 |
| Rotamer normality | -0.952 78 | -0.194 90 |
| Coarse packing | -0.645 29 | -0.701 27 |
| Fine packing | -1.571 29 | -1.597 28 |
| Bump severity | 0.002 87 | 0.001 92 |
| Hydrogen bond satisfaction | 0.916 72 | 0.917 73 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 7 |
| Side chains flipped | 0 |
| Waters removed | 14 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 30 |
| Residues fitting density worse | 0 |