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| Crystal Structure of Human ENPP4 with AMP |
| This entry was created with PDB-REDO version 8.03. |
| 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 | 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 | 0.1451 | 0.1486 |
| R-free | 0.1824 | 0.1731 |
| Bond length RMS Z-score | 1.104 | 0.992 |
| Bond angle RMS Z-score | 0.809 | 0.872 |
| Model quality | ||
| Ramachandran plot normality | -0.661 63 | -0.631 64 |
| Rotamer normality | -0.573 84 | -0.709 82 |
| Coarse packing | 0.778 90 | 0.645 87 |
| Fine packing | -2.080 12 | -2.131 11 |
| Bump severity | 0.419 2 | 0.351 3 |
| Hydrogen bond satisfaction | 0.873 23 | 0.878 27 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 8 |
| Side chains flipped | 1 |
| Waters removed | 69 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 4 |
| Residues fitting density worse | 1 |