| Newly identified epitope Mn2 from SARS-CoV M protein complexed withHLA-A*0201 |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 1.3 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 160.871 Å | b: 48.847 Å | c: 137.242 Å | α: 90.00° | β: 110.94° | γ: 90.00° |
| Resolution | 2.20 Å | Reflections | 50976 | Test set | 0 (0.0%) | ||
| R | 0.2050 | R-free | 0.2460 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.20 Å | Reflections | 50976 | Test set |
2528 (5.0%)
New test set, PDB-REDO compensated for this
|
||
| Twin | false | Radiation damage | 36 | ||||
| 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 | 0.2118 | 0.1789 |
| R-free |
0.2528
R-free was considered biased, the
estimated unbiased R-free was used
|
0.2200 |
| Bond length RMS Z-score | 0.507 | 0.316 |
| Bond angle RMS Z-score | 0.714 | 0.520 |
| Model quality | ||
| Ramachandran plot normality | -1.015 55 | 0.666 92 |
| Rotamer normality | -1.800 55 | -0.260 86 |
| Coarse packing | 0.258 61 | 0.428 67 |
| Fine packing | 0.533 91 | 0.980 95 |
| Bump severity | 0.013 49 | 0.006 68 |
| Hydrogen bond satisfaction | 0.906 58 | 0.910 64 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 30 |
| Side chains flipped | 0 |
| Waters removed | 57 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 29 |
| Residues fitting density worse | 0 |