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| Structure of post fusion core of 2019-nCoV S2 subunit |
| This entry was created with PDB-REDO version 8.04 using the deposited PDB model version 1.4 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 1 21 1 | a: 51.240 Å | b: 57.580 Å | c: 115.720 Å | α: 90.00° | β: 91.58° | γ: 90.00° |
| Resolution | 2.90 Å | Reflections | 14313 | Test set | 737 (5.1%) | ||
| R | 0.2593 | R-free | 0.2896 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.90 Å | Reflections | 14313 | Test set | 737 (5.1%) | ||
| 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 | 0.2605 | 0.2924 |
| R-free |
0.3167
R-free was considered biased, the
estimated unbiased R-free was used
|
0.3321 |
| Bond length RMS Z-score | 1.682 | 0.371 |
| Bond angle RMS Z-score | 0.963 | 0.571 |
| Model quality | ||
| Ramachandran plot normality | -3.539 12 | -1.754 34 |
| Rotamer normality | -3.982 26 | -2.982 40 |
| Coarse packing | 3.804 100 | 3.660 100 |
| Fine packing | 2.675 99 | 2.448 99 |
| Bump severity | 0.026 33 | 0.056 17 |
| Hydrogen bond satisfaction | 0.941 94 | 0.921 78 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 20 |
| Side chains flipped | 0 |
| Waters removed | 0 |
| Peptides flipped | 12 |
| Chiralities fixed | 0 |
| Residues fitting density better | 1 |
| Residues fitting density worse | 5 |