| Structure of BambL, a lectin from Burkholderia ambifaria, complexed with blood group B epitope |
| This entry was created with PDB-REDO version 8.10 using the deposited PDB model version 2.1 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 21 21 21 | a: 47.980 Å | b: 49.140 Å | c: 102.710 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
| Resolution | 1.75 Å | Reflections | 24088 | Test set | 1218 (5.1%) | ||
| R | 0.2080 | R-free | 0.2658 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.75 Å | Reflections | 24088 | Test set | 1218 (5.1%) | ||
| Twin | false | Radiation damage | 40 | ||||
| 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 | 0.2067 | 0.1880 |
| R-free | 0.2612 | 0.2259 |
| Bond length RMS Z-score | 1.206 | 0.542 |
| Bond angle RMS Z-score | 0.890 | 0.700 |
| Model quality | ||
| Ramachandran plot normality | -0.928 57 | -0.274 76 |
| Rotamer normality | -1.972 51 | -0.413 83 |
| Coarse packing | 1.136 88 | 1.204 89 |
| Fine packing | -1.993 14 | -2.027 14 |
| Bump severity | 0.007 65 | 0.001 90 |
| Hydrogen bond satisfaction | 0.878 27 | 0.864 19 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 1 |
| Side chains flipped | 0 |
| Waters removed | 19 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 1 |
| Residues fitting density worse | 0 |