This entry is not up to date with the most recent version of PDB-REDO.
Please log in
to request an update.
| 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 8.03. |
| 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 | N/A | ||||
| 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 | 0.2290 | 0.1999 |
| R-free |
0.2755
R-free was considered biased, the
estimated unbiased R-free was used
|
0.2577 |
| Bond length RMS Z-score | 0.762 | 0.179 |
| Bond angle RMS Z-score | 0.667 | 0.420 |
| Model quality | ||
| Ramachandran plot normality | -0.523 67 | -0.929 55 |
| Rotamer normality | -3.997 26 | -2.352 51 |
| Coarse packing | 1.289 97 | 1.071 95 |
| Fine packing | 1.647 97 | 2.255 98 |
| Bump severity | 0.012 53 | 0.003 82 |
| Hydrogen bond satisfaction | 0.929 86 | 0.940 93 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 3 |
| Side chains flipped | 3 |
| Waters removed | 9 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 2 |
| Residues fitting density worse | 0 |