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| The structure of I379E 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 1 21 1 | a: 72.383Å b: 114.366Å c: 130.462Å | α: 90.00° β: 92.04° γ: 90.00° | ||
| Resolution | 2.70 Å | Reflections | 56901 | Test set | 2808 (4.9%) |
| R | 0.2230 | R-free | 0.2692 | ||
| According to PDB-REDO | |||||
| Resolution | 2.70 Å | Reflections | 56901 | Test set | 2808 (4.9%) |
| 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 | 0.2433 | 0.2273 |
| R-free | 0.2820 | 0.2489 |
| Bond length RMS Z-score | 1.069 | 0.323 |
| Bond angle RMS Z-score | 0.778 | 0.540 |
| Model quality | ||
| Ramachandran plot normality | 0.184 84 | -1.506 40 |
| Rotamer normality | -4.215 23 | -1.993 58 |
| Coarse packing | N/A N/A | 0.533 84 |
| Fine packing | N/A N/A | -0.355 75 |
| Bump severity | 0.019 41 | 0.095 11 |
| Hydrogen bond satisfaction | 0.891 39 | 0.888 36 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 11 |
| Side chains built | 270 |
| Waters removed | 5 |
| Peptides flipped | 10 |
| Chiralities fixed | 0 |
| Residues fitting density better | 32 |
| Residues fitting density worse | 0 |