| Human ectonucleotide pyrophosphatase / phosphodiesterase 3 (ENPP3, NPP3, CD203c) |
| This entry was created with PDB-REDO version 8.12. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 21 21 21 | a: 96.184 Å | b: 133.640 Å | c: 167.430 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
| Resolution | 2.30 Å | Reflections | 87320 | Test set | 1918 (2.2%) | ||
| R | 0.1743 | R-free | 0.2138 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.30 Å | Reflections | 87320 | Test set | 1918 (2.2%) | ||
| Twin | false | Radiation damage | 62 | ||||
| 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 | 0.1858 | 0.1769 |
| R-free | 0.2232 | 0.2198 |
| Bond length RMS Z-score | 0.812 | 0.562 |
| Bond angle RMS Z-score | 0.707 | 0.712 |
| Model quality | ||
| Ramachandran plot normality | -1.301 47 | -1.303 47 |
| Rotamer normality | -1.203 68 | -1.638 58 |
| Coarse packing | -0.444 29 | -0.414 30 |
| Fine packing | -2.138 11 | -2.114 12 |
| Bump severity | 0.810 0 | 0.826 0 |
| Hydrogen bond satisfaction | 0.817 7 | 0.827 9 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 42 |
| Side chains flipped | 0 |
| Waters removed | 106 |
| Peptides flipped | 2 |
| Chiralities fixed | 0 |
| Residues fitting density better | 21 |
| Residues fitting density worse | 4 |