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| Crystal Structure of PGT121 Fab Bound to a complex-type sialylated N-glycan |
| This entry was created with PDB-REDO version 7.34. |
| From PDB header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 21 21 21 | a: 67.787 Å | b: 67.787 Å | c: 94.115 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
| Resolution | 2.40 Å | Reflections | 20573 | Test set | 1022 (5.0%) | ||
| R | 0.2010 | R-free | 0.2490 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.21 Å | Reflections | 20573 | Test set | 1022 (5.0%) | 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 | ||||
| PDB | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.2678 | 0.2074 |
| R-free | 0.2905 | 0.2688 |
| Bond length RMS Z-score | 0.278 | 0.565 |
| Bond angle RMS Z-score | 0.471 | 0.831 |
| Model quality | ||
| Ramachandran plot normality | 0.758 60 | 0.326 72 |
| Rotamer normality | 0.068 91 | 2.555 47 |
| Coarse packing | 0.002 62 | 0.014 61 |
| Fine packing | 0.234 78 | 0.171 85 |
| Bump severity | 0.306 3 | 0.186 6 |
| Hydrogen bond satisfaction | 0.924 81 | 0.931 88 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 3 |
| Side chains flipped | 0 |
| Waters removed | 13 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 8 |
| Residues fitting density worse | 0 |