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| Structure of the 2019-nCoV HR2 Domain |
| This entry was created with PDB-REDO version 8.04 using the deposited PDB model version 1.4 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 21 21 21 | a: 28.195 Å | b: 49.729 Å | c: 89.576 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
| Resolution | 2.47 Å | Reflections | 4862 | Test set | 0 (0.0%) | ||
| R | 0.2148 | R-free | 0.2580 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.47 Å | Reflections | 4862 | Test set |
500 (10.3%)
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 | 0.2383 | 0.2119 |
| R-free |
0.2880
R-free was considered biased, the
estimated unbiased R-free was used
|
0.2727 |
| Bond length RMS Z-score | 0.514 | 0.342 |
| Bond angle RMS Z-score | 0.689 | 0.474 |
| Model quality | ||
| Ramachandran plot normality | 3.053 100 | 4.448 100 |
| Rotamer normality | -4.134 24 | -2.492 49 |
| Coarse packing | 4.750 100 | 5.014 100 |
| Fine packing | 5.646 100 | 5.729 100 |
| Bump severity | 0.000 96 | 0.002 87 |
| Hydrogen bond satisfaction | 0.977 100 | 0.974 100 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 6 |
| Side chains flipped | 0 |
| Waters removed | 2 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 1 |
| Residues fitting density worse | 0 |