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| Structure of bacterial type II NADH dehydrogenase from Caldalkalibacillus thermarum complexed with a quinone inhibitor HQNO at 2.8A resolution |
| This entry was created with PDB-REDO version 8.04 using the deposited PDB model version 1.3 |
| From original header | |||||
|---|---|---|---|---|---|
| Spacegroup | P 1 21 1 | a: 72.847Å b: 114.342Å c: 130.061Å | α: 90.00° β: 91.17° γ: 90.00° | ||
| Resolution | 2.80 Å | Reflections | 52422 | Test set | 2595 (5.0%) |
| R | 0.2272 | R-free | 0.2681 | ||
| According to PDB-REDO | |||||
| Resolution | 2.80 Å | Reflections | 52422 | Test set | 2595 (5.0%) |
| 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 | 0.2453 | 0.2264 |
| R-free | 0.2805 | 0.2494 |
| Bond length RMS Z-score | 1.012 | 0.321 |
| Bond angle RMS Z-score | 0.717 | 0.534 |
| Model quality | ||
| Ramachandran plot normality | 0.370 87 | -2.072 28 |
| Rotamer normality | -3.127 38 | -2.563 47 |
| Coarse packing | -0.179 52 | 0.574 85 |
| Fine packing | -1.513 31 | -0.329 75 |
| Bump severity | 0.033 27 | 0.020 39 |
| Hydrogen bond satisfaction | 0.772 3 | 0.891 39 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 15 |
| Side chains built | 141 |
| Waters removed | 4 |
| Peptides flipped | 11 |
| Chiralities fixed | 0 |
| Residues fitting density better | 25 |
| Residues fitting density worse | 0 |