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| Crystal structure of the single chain variable fragment of the DH270.6 bnAb in complex with the Man9-V3 glycopeptide |
| This entry was created with PDB-REDO version 7.31. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 41 2 2 | a: 68.005 Å | b: 68.005 Å | c: 128.835 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
| Resolution | 2.17 Å | Reflections | 15873 | Test set | 813 (5.1%) | ||
| R | 0.2210 | R-free | 0.2780 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.17 Å | Reflections | 15873 | Test set | 813 (5.1%) | Twin | false |
| 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 | 0.2448 | 0.2186 |
| R-free | 0.2896 | 0.2705 |
| Bond length RMS Z-score | 0.272 | 0.709 |
| Bond angle RMS Z-score | 0.495 | 0.897 |
| Model quality | ||
| Ramachandran plot normality | -0.994 53 | -1.469 41 |
| Rotamer normality | -0.663 83 | -2.636 46 |
| Coarse packing | -0.977 17 | -1.008 16 |
| Fine packing | -1.048 51 | -0.967 54 |
| Bump severity | 0.390 2 | 0.549 1 |
| Hydrogen bond satisfaction | 0.868 20 | 0.885 33 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 5 |
| Side chains flipped | 1 |
| Waters removed | 3 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 4 |
| Residues fitting density worse | 0 |