| Murine ectonucleotide pyrophosphatase / phosphodiesterase 5 (ENPP5, NPP5), inactive (T72A), in complex with AMP |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 2.1 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 65 2 2 | a: 84.239 Å | b: 84.239 Å | c: 295.796 Å | α: 90.00° | β: 90.00° | γ: 120.00° |
| Resolution | 1.53 Å | Reflections | 81417 | Test set | 2000 (2.5%) | ||
| R | 0.1146 | R-free | 0.1449 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.53 Å | Reflections | 81417 | Test set | 2000 (2.5%) | ||
| Twin | false | Radiation damage | 69 | ||||
| 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 | 0.1245 | 0.1390 |
| R-free | 0.1529 | 0.1643 |
| Bond length RMS Z-score | 0.833 | 0.644 |
| Bond angle RMS Z-score | 0.909 | 0.760 |
| Model quality | ||
| Ramachandran plot normality | 0.217 86 | 0.061 83 |
| Rotamer normality | -0.093 88 | -0.109 88 |
| Coarse packing | 0.870 82 | 0.872 82 |
| Fine packing | -1.812 20 | -1.746 22 |
| Bump severity | 0.790 1 | 0.817 0 |
| Hydrogen bond satisfaction | 0.855 15 | 0.856 16 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 10 |
| Side chains flipped | 0 |
| Waters removed | 71 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 29 |