| Crystal structures of human E-NPP 1: bound to adenosine-5'-thio-monophosphate |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 1.3 |
| 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 | 81 | ||||
| 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 | 0.2090 | 0.1885 |
| R-free | 0.2409 | 0.2407 |
| Bond length RMS Z-score | 1.393 | 0.751 |
| Bond angle RMS Z-score | 0.977 | 0.893 |
| Model quality | ||
| Ramachandran plot normality | -2.142 29 | -3.333 14 |
| Rotamer normality | -2.987 32 | -3.890 20 |
| Coarse packing | -1.193 8 | -1.104 9 |
| Fine packing | -3.134 2 | -2.884 2 |
| Bump severity | 0.310 3 | 0.121 8 |
| Hydrogen bond satisfaction | 0.821 8 | 0.795 5 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 27 |
| Side chains flipped | 95 |
| Waters removed | 13 |
| Peptides flipped | 10 |
| Chiralities fixed | 0 |
| Residues fitting density better | 71 |
| Residues fitting density worse | 1 |