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| Crystal structure of the integral membrane diacylglycerol kinase - delta7 |
| This entry was created with PDB-REDO version 8.10 using the deposited PDB model version 1.6 |
| From original header | |||||
|---|---|---|---|---|---|
| Spacegroup | P 21 21 21 | a: 75.060Å b: 91.540Å c: 143.650Å | α: 90.00° β: 90.00° γ: 90.00° | ||
| Resolution | 2.05 Å | Reflections | 62602 | Test set | 3160 (5.0%) |
| R | 0.1959 | R-free | 0.2167 | ||
| According to PDB-REDO | |||||
| Resolution | 2.05 Å | Reflections | 62602 | Test set | 3160 (5.0%) |
| Twin | false | Radiation damage | 53 | ||
| 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 | 0.1973 | 0.1927 |
| R-free | 0.2163 | 0.2120 |
| Bond length RMS Z-score | 0.891 | 0.690 |
| Bond angle RMS Z-score | 0.700 | 0.730 |
| Model quality | ||
| Ramachandran plot normality | 1.137 96 | 2.636 99 |
| Rotamer normality | -0.223 86 | 0.719 96 |
| Coarse packing | 2.574 99 | 2.739 99 |
| Fine packing | 1.327 96 | 1.441 97 |
| Bump severity | 0.007 65 | 0.009 59 |
| Hydrogen bond satisfaction | 0.951 97 | 0.961 99 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 5 |
| Side chains built | 0 |
| Waters removed | 81 |
| Peptides flipped | 2 |
| Chiralities fixed | 0 |
| Residues fitting density better | 9 |
| Residues fitting density worse | 5 |