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| Human alkaline sphingomyelinase (ENPP7) in complex with phosphocholine |
| This entry was created with PDB-REDO version 7.32. |
| 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 | 0.1730 | R-free | 0.2080 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.40 Å | Reflections | 23513 | Test set | 1916 (8.1%) | ||
| 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 | 0.1899 | 0.1881 |
| R-free | 0.2201 | 0.2275 |
| Bond length RMS Z-score | 0.231 | 0.449 |
| Bond angle RMS Z-score | 0.591 | 0.732 |
| Model quality | ||
| Ramachandran plot normality | -1.770 34 | -1.485 40 |
| Rotamer normality | -1.876 60 | -2.511 48 |
| Coarse packing | -0.884 20 | -0.993 16 |
| Fine packing | -2.835 3 | -2.673 4 |
| Bump severity | 0.842 0 | 0.173 6 |
| Hydrogen bond satisfaction | 0.861 17 | 0.873 23 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 5 |
| Side chains flipped | 0 |
| Waters removed | 7 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 1 |