| 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 8.13 using the deposited PDB model version 2.2 |
| 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 | 0.2778 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.17 Å | Reflections | 15873 | Test set | 813 (5.1%) | ||
| Twin | false | Radiation damage | 79 | ||||
| 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 | 0.2455 | 0.2092 |
| R-free | 0.2914 | 0.2725 |
| Bond length RMS Z-score | 0.586 | 0.513 |
| Bond angle RMS Z-score | 0.683 | 0.709 |
| Model quality | ||
| Ramachandran plot normality | -0.860 59 | -1.179 50 |
| Rotamer normality | -0.661 79 | -1.591 59 |
| Coarse packing | -0.843 15 | -0.823 16 |
| Fine packing | -0.686 65 | -0.479 72 |
| Bump severity | 0.358 3 | 0.421 2 |
| Hydrogen bond satisfaction | 0.848 13 | 0.878 27 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 5 |
| Side chains flipped | 1 |
| Waters removed | 2 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 14 |
| Residues fitting density worse | 0 |