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| The crystal structure of Nsp9 RNA binding protein of SARS CoV-2 |
| This entry was created with PDB-REDO version 8.04 using the deposited PDB model version 1.3 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 61 2 2 | a: 89.883 Å | b: 89.883 Å | c: 132.587 Å | α: 90.00° | β: 90.00° | γ: 120.00° |
| Resolution | 2.95 Å | Reflections | 6937 | Test set | 0 (0.0%) | ||
| R | 0.2398 | R-free | 0.2760 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.95 Å | Reflections | 6937 | Test set |
709 (10.2%)
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 | 0.2702 | 0.2259 |
| R-free |
0.3270
R-free was considered biased, the
estimated unbiased R-free was used
|
0.3034 |
| Bond length RMS Z-score | 0.445 | 0.451 |
| Bond angle RMS Z-score | 0.608 | 0.748 |
| Model quality | ||
| Ramachandran plot normality | -2.331 24 | -3.176 15 |
| Rotamer normality | -4.527 20 | -6.135 8 |
| Coarse packing | -0.665 28 | -0.894 19 |
| Fine packing | -1.225 43 | -1.109 48 |
| Bump severity | 0.044 21 | 0.161 7 |
| Hydrogen bond satisfaction | 0.886 34 | 0.869 21 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 3 |
| Side chains built | 11 |
| Waters removed | 0 |
| Peptides flipped | 6 |
| Chiralities fixed | 0 |
| Residues fitting density better | 19 |
| Residues fitting density worse | 4 |