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| Human ectonucleotide pyrophosphatase / phosphodiesterase 3 (ENPP3, NPP3, CD203c), inactive (T205A), N594S, with alpha,beta-methylene-ATP (AMPCPP) |
| This entry was created with PDB-REDO version 8.12 using the deposited PDB model version 2.2 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 1 21 1 | a: 78.656 Å | b: 169.457 Å | c: 79.062 Å | α: 90.00° | β: 103.87° | γ: 90.00° |
| Resolution | 1.94 Å | Reflections | 124298 | Test set | 1987 (1.6%) | ||
| R | 0.1657 | R-free | 0.1974 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.94 Å | Reflections | 124298 | Test set | 1987 (1.6%) | ||
| Twin | true | Radiation damage | 42 | ||||
| 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 | 0.1673 | 0.1650 |
| R-free | 0.1986 | 0.1911 |
| Bond length RMS Z-score | 0.825 | 0.447 |
| Bond angle RMS Z-score | 0.724 | 0.603 |
| Model quality | ||
| Ramachandran plot normality | -1.524 41 | -0.790 61 |
| Rotamer normality | -1.737 56 | -1.112 70 |
| Coarse packing | -0.495 27 | -0.406 31 |
| Fine packing | -2.160 11 | -2.023 14 |
| Bump severity | 0.549 1 | 0.550 1 |
| Hydrogen bond satisfaction | 0.822 8 | 0.819 7 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 26 |
| Side chains built | 0 |
| Waters removed | 65 |
| Peptides flipped | 3 |
| Chiralities fixed | 0 |
| Residues fitting density better | 3 |
| Residues fitting density worse | 2 |