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| Structure of ENPP6, a choline-specific glycerophosphodiester-phosphodiesterase in complex with phosphocholine |
| This entry was created with PDB-REDO version 7.32. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 1 | a: 63.620 Å | b: 68.849 Å | c: 69.761 Å | α: 60.59° | β: 86.99° | γ: 68.10° |
| Resolution | 1.80 Å | Reflections | 81806 | Test set | 4091 (5.0%) | ||
| R | 0.1750 | R-free | 0.2110 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.80 Å | Reflections | 81806 | Test set | 4091 (5.0%) | ||
| Twin | false | Radiation damage | N/A | ||||
| 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 | 0.1794 | 0.1667 |
| R-free | 0.2099 | 0.1889 |
| Bond length RMS Z-score | 0.319 | 0.537 |
| Bond angle RMS Z-score | 0.647 | 0.755 |
| Model quality | ||
| Ramachandran plot normality | -0.248 74 | 0.194 84 |
| Rotamer normality | -1.135 75 | -0.482 86 |
| Coarse packing | -0.125 55 | -0.157 54 |
| Fine packing | -2.119 11 | -1.753 22 |
| Bump severity | 0.464 2 | 0.074 13 |
| Hydrogen bond satisfaction | 0.887 35 | 0.898 48 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 8 |
| Side chains flipped | 5 |
| Waters removed | 50 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 9 |
| Residues fitting density worse | 1 |