| Human alkaline sphingomyelinase (ENPP7) 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 31 2 1 | a: 104.223 Å | b: 104.223 Å | c: 113.893 Å | α: 90.00° | β: 90.00° | γ: 120.00° |
| Resolution | 2.40 Å | Reflections | 23513 | Test set | 1916 (8.1%) | ||
| R | 0.1727 | R-free | 0.2081 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.40 Å | Reflections | 23513 | Test set | 1916 (8.1%) | ||
| Twin | false | Radiation damage | 72 | ||||
| PDB-REDO files | |||||||
| Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
|||||
| Links | |||||||
| PDBe | RCSB PDB | 3D bionotes | Proteopedia | ||||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.1908 | 0.1782 |
| R-free | 0.2214 | 0.2182 |
| Bond length RMS Z-score | 0.544 | 0.344 |
| Bond angle RMS Z-score | 0.688 | 0.548 |
| Model quality | ||
| Ramachandran plot normality | -1.585 40 | -1.181 50 |
| Rotamer normality | -1.876 53 | -2.188 47 |
| Coarse packing | -0.152 42 | -0.249 37 |
| Fine packing | -2.529 5 | -2.461 6 |
| Bump severity | 0.838 0 | 0.856 0 |
| Hydrogen bond satisfaction | 0.838 11 | 0.845 12 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 5 |
| Side chains flipped | 0 |
| Waters removed | 13 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 1 |
| Residues fitting density worse | 0 |