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| The structure of G164E variant of type II NADH dehydrogenase from Caldalkalibacillus thermarum |
| This entry was created with PDB-REDO version 8.04 using the deposited PDB model version 1.2 |
| From original header | |||||
|---|---|---|---|---|---|
| Spacegroup | P 41 21 2 | a: 93.098Å b: 93.098Å c: 248.483Å | α: 90.00° β: 90.00° γ: 90.00° | ||
| Resolution | 3.20 Å | Reflections | 18718 | Test set | 958 (5.1%) |
| R | 0.2025 | R-free | 0.2338 | ||
| According to PDB-REDO | |||||
| Resolution | 3.20 Å | Reflections | 18718 | Test set | 958 (5.1%) |
| 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 | 0.2328 | 0.2165 |
| R-free | 0.2464 | 0.2451 |
| Bond length RMS Z-score | 1.026 | 0.393 |
| Bond angle RMS Z-score | 0.744 | 0.627 |
| Model quality | ||
| Ramachandran plot normality | 1.065 95 | -2.827 18 |
| Rotamer normality | -5.454 12 | -4.152 24 |
| Coarse packing | N/A N/A | 0.248 74 |
| Fine packing | N/A N/A | -0.797 61 |
| Bump severity | 0.041 22 | 0.043 22 |
| Hydrogen bond satisfaction | 0.868 20 | 0.862 18 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 7 |
| Side chains built | 133 |
| Waters removed | 1 |
| Peptides flipped | 12 |
| Chiralities fixed | 0 |
| Residues fitting density better | 27 |
| Residues fitting density worse | 0 |