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| Crystal structure of the integral membrane diacylglycerol kinase - delta4 |
| This entry was created with PDB-REDO version 8.08 using the deposited PDB model version 1.6 |
| From original header | |||||
|---|---|---|---|---|---|
| Spacegroup | P 31 2 1 | a: 72.740Å b: 72.740Å c: 198.990Å | α: 90.00° β: 90.00° γ: 120.00° | ||
| Resolution | 3.10 Å | Reflections | 10993 | Test set | 526 (4.8%) |
| R | 0.2320 | R-free | 0.2581 | ||
| According to PDB-REDO | |||||
| Resolution | 3.10 Å | Reflections | 10993 | Test set | 526 (4.8%) |
| 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 | 0.2499 | 0.2288 |
| R-free | 0.2641 | 0.2708 |
| Bond length RMS Z-score | 0.441 | 0.665 |
| Bond angle RMS Z-score | 0.424 | 0.875 |
| Model quality | ||
| Ramachandran plot normality | -2.599 22 | -4.521 6 |
| Rotamer normality | -1.912 53 | -5.005 10 |
| Coarse packing | 2.575 99 | 2.467 99 |
| Fine packing | 1.509 97 | -0.034 82 |
| Bump severity | 0.004 76 | 0.079 12 |
| Hydrogen bond satisfaction | 0.942 94 | 0.938 92 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 3 |
| Side chains built | 0 |
| Waters removed | 0 |
| Peptides flipped | 8 |
| Chiralities fixed | 0 |
| Residues fitting density better | 11 |
| Residues fitting density worse | 0 |