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| Crystal structure of the Orexin-1 receptor in complex with EMPA |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 1.5 |
| From original header | |||||
|---|---|---|---|---|---|
| Spacegroup | I 1 2 1 | a: 57.907Å b: 158.891Å c: 182.354Å | α: 90.00° β: 95.77° γ: 90.00° | ||
| Resolution | 2.11 Å | Reflections | 95566 | Test set | 4769 (5.0%) |
| R | 0.1880 | R-free | 0.2080 | ||
| According to PDB-REDO | |||||
| Resolution | 2.09 Å | Reflections | 95566 | Test set | 4769 (5.0%) |
| Twin | false | Radiation damage | 88 | ||
| PDB-REDO files | |||||
| Re-refined and rebuilt structure |
Re-refined (only) structure
|
All files
(compressed) |
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| Links | |||||
| PDBe | RCSB PDB | Proteopedia | |||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.2505 | 0.2309 |
| R-free | 0.2661 | 0.2614 |
| Bond length RMS Z-score | 1.220 | 0.418 |
| Bond angle RMS Z-score | 0.940 | 0.598 |
| Model quality | ||
| Ramachandran plot normality | -1.140 51 | -2.610 21 |
| Rotamer normality | -1.537 60 | -1.704 57 |
| Coarse packing | 1.612 94 | 1.876 96 |
| Fine packing | 1.238 96 | 1.191 96 |
| Bump severity | 0.009 59 | 0.008 62 |
| Hydrogen bond satisfaction | 0.933 89 | 0.927 84 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 5 |
| Side chains built | 0 |
| Waters removed | 52 |
| Peptides flipped | 1 |
| Chiralities fixed | 0 |
| Residues fitting density better | 65 |
| Residues fitting density worse | 1 |