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| The structure of type II NADH dehydrogenase from Caldalkalibacillus thermarum complexed with NAD+ at 3.0 angstrom resolution. |
| 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: 72.061Å b: 114.206Å c: 130.957Å | α: 90.00° β: 91.53° γ: 90.00° | ||
| Resolution | 3.00 Å | Reflections | 42161 | Test set | 2134 (5.1%) |
| R | 0.2373 | R-free | 0.2542 | ||
| According to PDB-REDO | |||||
| Resolution | 3.00 Å | Reflections | 42161 | Test set | 2134 (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 | 0.2521 | 0.2083 |
| R-free | 0.2611 | 0.2338 |
| Bond length RMS Z-score | 1.247 | 0.356 |
| Bond angle RMS Z-score | 0.713 | 0.566 |
| Model quality | ||
| Ramachandran plot normality | 0.249 85 | -2.255 25 |
| Rotamer normality | -3.618 30 | -2.888 42 |
| Coarse packing | N/A N/A | 0.589 85 |
| Fine packing | N/A N/A | -0.588 68 |
| Bump severity | 0.031 28 | 0.051 19 |
| Hydrogen bond satisfaction | 0.862 18 | 0.869 21 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 10 |
| Side chains built | 255 |
| Waters removed | 3 |
| Peptides flipped | 17 |
| Chiralities fixed | 0 |
| Residues fitting density better | 65 |
| Residues fitting density worse | 0 |