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| Structure of linear gramicidin D obtained using Type I crystals grown in a lipid cubic phase. |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 2.2 |
| From original header | |||||
|---|---|---|---|---|---|
| Spacegroup | P 1 21 1 | a: 30.500Å b: 62.560Å c: 30.530Å | α: 90.00° β: 99.97° γ: 90.00° | ||
| Resolution | 1.70 Å | Reflections | 11735 | Test set | 604 (5.1%) |
| R | 0.1790 | R-free | 0.2140 | ||
| According to PDB-REDO | |||||
| Resolution | 1.70 Å | Reflections | 11735 | Test set | 604 (5.1%) |
| Twin | true | Radiation damage | N/A | ||
| PDB-REDO files | |||||
| Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
|||
| Links | |||||
| PDBe | RCSB PDB | Proteopedia | |||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.1785 | 0.1647 |
| R-free | 0.2158 | 0.1798 |
| Bond length RMS Z-score | 1.387 | 0.657 |
| Bond angle RMS Z-score | 0.996 | 0.695 |
| Model quality | ||
| Ramachandran plot normality | -12.949 0 | -13.072 0 |
| Rotamer normality | -5.915 5 | -6.560 3 |
| 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 | 0.400 0 | 0.500 0 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 0 |
| Side chains built | 0 |
| Waters removed | 0 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 67 |
| Residues fitting density worse | 0 |