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| Crystal structure of the integral membrane diacylglycerol kinase DgkA- 9.9, delta 4 |
| This entry was created with PDB-REDO version 8.04 using the deposited PDB model version 1.5 |
| From original header | |||||
|---|---|---|---|---|---|
| Spacegroup | P 31 2 1 | a: 72.780Å b: 72.780Å c: 199.280Å | α: 90.00° β: 90.00° γ: 120.00° | ||
| Resolution | 3.25 Å | Reflections | 10170 | Test set | 0 (0.0%) |
| R | 0.2554 | R-free | 0.2915 | ||
| According to PDB-REDO | |||||
| Resolution | 3.25 Å | Reflections | 10170 | Test set |
957 (9.4%)
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 | Proteopedia | |||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.2674 | 0.2350 |
| R-free |
0.3238
R-free was considered biased, the
estimated unbiased R-free was used
|
0.2780 |
| Bond length RMS Z-score | 0.383 | 0.459 |
| Bond angle RMS Z-score | 0.399 | 0.662 |
| Model quality | ||
| Ramachandran plot normality | -3.008 17 | -4.923 5 |
| Rotamer normality | -2.326 44 | -5.347 7 |
| 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 | N/A N/A | N/A N/A |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 2 |
| Side chains built | 0 |
| Waters removed | 0 |
| Peptides flipped | 6 |
| Chiralities fixed | 0 |
| Residues fitting density better | 14 |
| Residues fitting density worse | 1 |