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| Crystal structure of the f15w mutant of apo-cellular retinoic acid binding protein type ii at 1.51 angstroms resolution |
| This entry was created with PDB-REDO version 8.04. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 1 | a: 34.582 Å | b: 37.030 Å | c: 58.693 Å | α: 102.00° | β: 106.12° | γ: 93.00° |
| Resolution | 1.51 Å | Reflections | 39495 | Test set | 3946 (10%) | ||
| R | 0.1740 | R-free | 0.2400 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.51 Å | Reflections | 39495 | Test set | 3946 (10%) | ||
| 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 | 0.1766 | 0.1771 |
| R-free | 0.2440 | 0.2272 |
| Bond length RMS Z-score | 1.061 | 0.766 |
| Bond angle RMS Z-score | 0.851 | 0.823 |
| Model quality | ||
| Ramachandran plot normality | 1.108 96 | 1.442 97 |
| Rotamer normality | -2.307 45 | -1.680 57 |
| Coarse packing | N/A N/A | N/A N/A |
| Fine packing | N/A N/A | N/A N/A |
| Bump severity | 0.000 95 | 0.000 95 |
| Hydrogen bond satisfaction | N/A N/A | N/A N/A |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 4 |
| Side chains flipped | 12 |
| Waters removed | 43 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 2 |
| Residues fitting density worse | 0 |