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| Crystal structure of the integral membrane diacylglycerol kinase - form 2 |
| 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: 72.820Å b: 72.820Å c: 195.670Å | α: 90.00° β: 90.00° γ: 120.00° | ||
| Resolution | 2.92 Å | Reflections | 13522 | Test set | 644 (4.8%) |
| R | 0.2479 | R-free | 0.2809 | ||
| According to PDB-REDO | |||||
| Resolution | 2.92 Å | Reflections | 13522 | Test set | 644 (4.8%) |
| Twin | false | Radiation damage | N/A | ||
| 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 | 0.2532 | 0.2145 |
| R-free | 0.2905 | 0.2533 |
| Bond length RMS Z-score | 0.714 | 0.703 |
| Bond angle RMS Z-score | 0.429 | 0.823 |
| Model quality | ||
| Ramachandran plot normality | -2.659 21 | -1.635 39 |
| Rotamer normality | -2.321 44 | -2.494 41 |
| 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 | 0 |
| Side chains built | 0 |
| Waters removed | 0 |
| Peptides flipped | 4 |
| Chiralities fixed | 0 |
| Residues fitting density better | 21 |
| Residues fitting density worse | 0 |