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| His 62 mutant of the lectin binding domain of lectinolysin complexed with Lewis y |
| This entry was created with PDB-REDO version 8.08 using the deposited PDB model version 2.1 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 43 21 2 | a: 67.097 Å | b: 67.097 Å | c: 99.432 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
| Resolution | 1.60 Å | Reflections | 30495 | Test set | 1536 (5.0%) | ||
| R | 0.1684 | R-free | 0.1902 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.60 Å | Reflections | 30495 | Test set | 1536 (5.0%) | ||
| Twin | false | Radiation damage | 55 | ||||
| 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 | 0.1626 | 0.1279 |
| R-free | 0.1762 | 0.1463 |
| Bond length RMS Z-score | 2.100 | 0.741 |
| Bond angle RMS Z-score | 1.478 | 0.707 |
| Model quality | ||
| Ramachandran plot normality | 0.561 91 | 0.892 94 |
| Rotamer normality | 0.567 95 | 0.713 96 |
| Coarse packing | 1.030 86 | 0.960 84 |
| Fine packing | -0.915 57 | -0.658 66 |
| Bump severity | 0.275 4 | 0.216 5 |
| Hydrogen bond satisfaction | 0.884 32 | 0.920 77 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 4 |
| Side chains built | 0 |
| Waters removed | 8 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 30 |
| Residues fitting density worse | 0 |