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| Crystal structure of the integral membrane diacylglycerol kinase - wild-type |
| 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: 74.970Å b: 74.970Å c: 196.900Å | α: 90.00° β: 90.00° γ: 120.00° | ||
| Resolution | 3.70 Å | Reflections | 7076 | Test set | 0 (0.0%) |
| R | 0.2848 | R-free | 0.3118 | ||
| According to PDB-REDO | |||||
| Resolution | 3.70 Å | Reflections | 7076 | Test set |
743 (10.5%)
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 | 0.3129 | 0.2126 |
| R-free |
0.3804
R-free was considered biased, the
estimated unbiased R-free was used
|
0.2672 |
| Bond length RMS Z-score | 0.525 | 0.661 |
| Bond angle RMS Z-score | 0.523 | 0.855 |
| Model quality | ||
| Ramachandran plot normality | -4.301 7 | -7.082 1 |
| Rotamer normality | -4.919 10 | -5.448 7 |
| Coarse packing | 1.877 96 | 2.155 98 |
| Fine packing | 0.426 90 | -0.039 82 |
| Bump severity | 0.003 81 | 0.060 15 |
| Hydrogen bond satisfaction | 0.908 61 | 0.902 53 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 1 |
| Side chains built | 0 |
| Waters removed | 0 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 86 |
| Residues fitting density worse | 0 |