| Crystal Structure of PGT121 Fab Bound to a complex-type sialylated N-glycan |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 2.2 |
| From original 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 | 20572 | Test set | 1022 (5.0%) | ||
| R | 0.2010 | R-free | 0.2490 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.21 Å | Reflections | 20572 | Test set | 1022 (5.0%) | ||
| Twin | false | Radiation damage | 73 | ||||
| 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 | 0.2680 | 0.1941 |
| R-free | 0.2907 | 0.2534 |
| Bond length RMS Z-score | 0.738 | 0.189 |
| Bond angle RMS Z-score | 0.700 | 0.446 |
| Model quality | ||
| Ramachandran plot normality | -0.646 65 | -0.363 73 |
| Rotamer normality | -0.080 89 | -0.121 88 |
| Coarse packing | 0.227 59 | 0.227 59 |
| Fine packing | 0.035 83 | 0.255 87 |
| Bump severity | 0.301 3 | 0.252 4 |
| Hydrogen bond satisfaction | 0.910 64 | 0.916 72 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 6 |
| Side chains flipped | 0 |
| Waters removed | 13 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 8 |
| Residues fitting density worse | 0 |