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| Structure of bacterial type II NADH dehydrogenase from Caldalkalibacillus thermarum at 2.15A resolution |
| This entry was created with PDB-REDO version 8.08 using the deposited PDB model version 1.4 |
| From original header | |||||
|---|---|---|---|---|---|
| Spacegroup | P 1 21 1 | a: 72.804Å b: 113.570Å c: 129.781Å | α: 90.00° β: 91.02° γ: 90.00° | ||
| Resolution | 2.15 Å | Reflections | 105261 | Test set | 5250 (5.0%) |
| R | 0.2079 | R-free | 0.2379 | ||
| According to PDB-REDO | |||||
| Resolution | 2.15 Å | Reflections | 105261 | Test set | 5250 (5.0%) |
| Twin | false | Radiation damage | 74 | ||
| 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 | 0.2209 | 0.2000 |
| R-free | 0.2455 | 0.2289 |
| Bond length RMS Z-score | 0.975 | 0.377 |
| Bond angle RMS Z-score | 0.669 | 0.564 |
| Model quality | ||
| Ramachandran plot normality | 0.091 84 | -0.138 79 |
| Rotamer normality | 0.138 91 | -0.550 81 |
| Coarse packing | 0.441 68 | 0.877 82 |
| Fine packing | -0.927 56 | -0.058 82 |
| Bump severity | 0.009 59 | 0.010 56 |
| Hydrogen bond satisfaction | 0.725 2 | 0.914 69 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 20 |
| Side chains built | 101 |
| Waters removed | 14 |
| Peptides flipped | 2 |
| Chiralities fixed | 0 |
| Residues fitting density better | 32 |
| Residues fitting density worse | 0 |