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| The structure of type II NADH dehydrogenase from Caldalkalibacillus thermarum complexed with NAD+ at 2.5 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: 72.883Å b: 114.014Å c: 130.638Å | α: 90.00° β: 91.76° γ: 90.00° | ||
| Resolution | 2.50 Å | Reflections | 73878 | Test set | 3726 (5.0%) |
| R | 0.2140 | R-free | 0.2440 | ||
| According to PDB-REDO | |||||
| Resolution | 2.50 Å | Reflections | 73878 | Test set | 3726 (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 | 0.2317 | 0.1899 |
| R-free | 0.2624 | 0.2211 |
| Bond length RMS Z-score | 1.087 | 0.504 |
| Bond angle RMS Z-score | 0.691 | 0.674 |
| Model quality | ||
| Ramachandran plot normality | 0.798 92 | -1.023 53 |
| Rotamer normality | -2.210 54 | -1.460 69 |
| Coarse packing | 0.124 68 | 0.753 89 |
| Fine packing | -1.621 27 | -0.127 80 |
| Bump severity | 0.019 41 | 0.012 53 |
| Hydrogen bond satisfaction | 0.893 41 | 0.898 48 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 12 |
| Side chains built | 157 |
| Waters removed | 34 |
| Peptides flipped | 14 |
| Chiralities fixed | 0 |
| Residues fitting density better | 135 |
| Residues fitting density worse | 0 |