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| The Crystal Structure of the Phosphodiesterase 2A Catalytic Domain |
| This entry was created with PDB-REDO version 8.01. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 2 2 21 | a: 90.033 Å | b: 102.549 Å | c: 81.598 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
| Resolution | 1.70 Å | Reflections | 37389 | Test set | 3413 (9.1%) | ||
| R | 0.2060 | R-free | 0.2370 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.75 Å | Reflections | 37389 | Test set | 3413 (9.1%) | ||
| 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 | 0.1963 | 0.1690 |
| R-free | 0.2259 | 0.2063 |
| Bond length RMS Z-score | 0.218 | 0.453 |
| Bond angle RMS Z-score | 0.584 | 0.703 |
| Model quality | ||
| Ramachandran plot normality | -0.333 72 | 0.950 94 |
| Rotamer normality | -1.134 75 | -0.189 90 |
| Coarse packing | 1.952 99 | 2.070 99 |
| Fine packing | -1.073 50 | -0.435 72 |
| Bump severity | 0.009 61 | 0.011 56 |
| Hydrogen bond satisfaction | 0.907 60 | 0.902 53 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 8 |
| Side chains flipped | 13 |
| Waters removed | 12 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 26 |
| Residues fitting density worse | 0 |