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| Crystal structures of human E-NPP 1: bound to adenosine-5'-thio-monophosphate |
| This entry was created with PDB-REDO version 7.33. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 21 21 21 | a: 83.010 Å | b: 160.143 Å | c: 209.632 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
| Resolution | 2.65 Å | Reflections | 81930 | Test set | 4208 (5.1%) | ||
| R | 0.2070 | R-free | 0.2390 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.65 Å | Reflections | 81930 | Test set | 4208 (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 | 0.2083 | 0.2034 |
| R-free | 0.2403 | 0.2308 |
| Bond length RMS Z-score | 0.661 | 0.386 |
| Bond angle RMS Z-score | 0.982 | 0.695 |
| Model quality | ||
| Ramachandran plot normality | -2.273 25 | -1.873 32 |
| Rotamer normality | -2.951 41 | -2.850 42 |
| Coarse packing | -1.968 3 | -1.688 5 |
| Fine packing | -3.176 1 | -2.609 4 |
| Bump severity | 0.312 3 | 0.156 7 |
| Hydrogen bond satisfaction | 0.831 9 | 0.831 9 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 17 |
| Side chains flipped | 95 |
| Waters removed | 5 |
| Peptides flipped | 16 |
| Chiralities fixed | 0 |
| Residues fitting density better | 47 |
| Residues fitting density worse | 3 |