This entry is not up to date with the most recent version of PDB-REDO.
Please log in
to request an update.
| Structure of delta4-DgkA-apo in 9.9 MAG |
| This entry was created with PDB-REDO version 8.08 using the deposited PDB model version 1.5 |
| From original header | |||||
|---|---|---|---|---|---|
| Spacegroup | P 31 2 1 | a: 72.800Å b: 72.800Å c: 199.320Å | α: 90.00° β: 90.00° γ: 120.00° | ||
| Resolution | 3.15 Å | Reflections | 11125 | Test set | 566 (5.1%) |
| R | 0.2244 | R-free | 0.2681 | ||
| According to PDB-REDO | |||||
| Resolution | 3.15 Å | Reflections | 11125 | Test set | 566 (5.1%) |
| Twin | false | Radiation damage |
98
Data shows severe radiation damage
|
||
| 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 | 0.2404 | 0.2173 |
| R-free | 0.2668 | 0.2508 |
| Bond length RMS Z-score | 0.885 | 0.350 |
| Bond angle RMS Z-score | 0.728 | 0.540 |
| Model quality | ||
| Ramachandran plot normality | -3.538 12 | -2.850 19 |
| Rotamer normality | -4.597 13 | -4.409 14 |
| Coarse packing | 2.326 98 | 2.482 99 |
| Fine packing | -0.051 82 | -0.027 82 |
| Bump severity | 0.027 30 | 0.070 13 |
| Hydrogen bond satisfaction | 0.941 94 | 0.919 76 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 1 |
| Side chains built | 0 |
| Waters removed | 0 |
| Peptides flipped | 6 |
| Chiralities fixed | 0 |
| Residues fitting density better | 13 |
| Residues fitting density worse | 1 |