| Crystal Structure of Human ENPP4 with AMP |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 2.2 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 181.533 Å | b: 51.143 Å | c: 52.741 Å | α: 90.00° | β: 102.38° | γ: 90.00° |
| Resolution | 1.54 Å | Reflections | 69525 | Test set | 3515 (5.1%) | ||
| R | 0.1402 | R-free | 0.1844 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.54 Å | Reflections | 69525 | Test set | 3515 (5.1%) | ||
| Twin | false | Radiation damage | 31 | ||||
| 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 | 0.1476 | 0.1530 |
| R-free | 0.1835 | 0.1744 |
| Bond length RMS Z-score | 1.110 | 0.739 |
| Bond angle RMS Z-score | 0.829 | 0.748 |
| Model quality | ||
| Ramachandran plot normality | -0.661 65 | -0.425 72 |
| Rotamer normality | -0.573 80 | -0.563 81 |
| Coarse packing | 0.778 79 | 0.666 76 |
| Fine packing | -1.135 47 | -1.326 39 |
| Bump severity | 0.418 2 | 0.402 2 |
| Hydrogen bond satisfaction | 0.869 21 | 0.868 21 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 7 |
| Side chains flipped | 1 |
| Waters removed | 72 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 5 |
| Residues fitting density worse | 2 |