| Structure of ENPP6, a choline-specific glycerophosphodiester-phosphodiesterase in complex with phosphocholine |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 2.1 |
| 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 | 0.1748 | R-free | 0.2111 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.80 Å | Reflections | 81806 | Test set | 4091 (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 | 0.1810 | 0.1626 |
| R-free | 0.2106 | 0.1844 |
| Bond length RMS Z-score | 0.823 | 0.357 |
| Bond angle RMS Z-score | 0.781 | 0.561 |
| Model quality | ||
| Ramachandran plot normality | -0.082 80 | 0.386 89 |
| Rotamer normality | -1.135 69 | -0.072 89 |
| Coarse packing | 0.611 74 | 0.579 73 |
| Fine packing | -1.565 29 | -1.355 38 |
| Bump severity | 0.463 2 | 0.469 2 |
| Hydrogen bond satisfaction | 0.852 14 | 0.865 19 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 8 |
| Side chains flipped | 5 |
| Waters removed | 48 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 41 |
| Residues fitting density worse | 0 |