| CRYSTAL STRUCTURE OF CELLULAR RETINOIC-ACID-BINDING PROTEINS I AND II IN COMPLEX WITH ALL-TRANS-RETINOIC ACID AND A SYNTHETIC RETINOID |
| This entry was created with PDB-REDO version 8.12 using the deposited PDB model version 1.3 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 21 21 21 | a: 45.650 Å | b: 47.560 Å | c: 77.610 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
| Resolution | 1.80 Å | Reflections | 14678 | Test set | 1496 (10.2%) | ||
| R | 0.2000 | R-free | 0.2370 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.80 Å | Reflections | 14678 | Test set | 1496 (10.2%) | ||
| Twin | false | Radiation damage | 61 | ||||
| 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 | 0.1782 | 0.1497 |
| R-free |
0.2093
R-free was considered biased, the
estimated unbiased R-free was used
|
0.1943 |
| Bond length RMS Z-score | 0.734 | 0.747 |
| Bond angle RMS Z-score | 0.782 | 0.811 |
| Model quality | ||
| Ramachandran plot normality | 1.399 97 | 1.634 98 |
| Rotamer normality | -0.797 76 | 0.047 90 |
| Coarse packing | 1.397 92 | 1.412 92 |
| Fine packing | 3.252 99 | 3.424 99 |
| Bump severity | 0.000 95 | 0.000 95 |
| Hydrogen bond satisfaction | 0.962 99 | 0.955 98 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 2 |
| Side chains flipped | 0 |
| Waters removed | 7 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 5 |
| Residues fitting density worse | 0 |