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| Crystal Structure of the R111K:R132L:Y134F:T54V:R59W Mutant of the Cellular Retinoic Acid Binding Protein Type II in Complex with All-Trans Retinal at 2.58 Angstrom Resolution |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 1.3 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 31 2 1 | a: 56.455 Å | b: 56.455 Å | c: 108.192 Å | α: 90.00° | β: 90.00° | γ: 120.00° |
| Resolution | 2.58 Å | Reflections | 6566 | Test set | 0 (0.0%) | ||
| R | 0.2240 | R-free | 0.2878 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.58 Å | Reflections | 6566 | Test set |
647 (9.9%)
New test set, PDB-REDO compensated for this
|
||
| Twin | false | Radiation damage | 82 | ||||
| PDB-REDO files | |||||||
| Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
|||||
| Links | |||||||
| PDBe | RCSB PDB | 3D bionotes | Proteopedia | ||||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.2320 | 0.2034 |
| R-free |
0.2791
R-free was considered biased, the
estimated unbiased R-free was used
|
0.2645 |
| Bond length RMS Z-score | 0.759 | 0.174 |
| Bond angle RMS Z-score | 0.665 | 0.415 |
| Model quality | ||
| Ramachandran plot normality | -0.523 69 | -0.808 61 |
| Rotamer normality | -3.997 19 | -1.944 52 |
| Coarse packing | 1.289 90 | 1.107 87 |
| Fine packing | 2.219 98 | 2.828 99 |
| Bump severity | 0.012 51 | 0.003 81 |
| Hydrogen bond satisfaction | 0.921 78 | 0.933 89 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 2 |
| Side chains built | 3 |
| Waters removed | 10 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 1 |
| Residues fitting density worse | 0 |