| Structure of caa3-type cytochrome oxidase |
| This entry was created with PDB-REDO version 8.22 using the deposited PDB model version 2.0 |
| From original header | |||||
|---|---|---|---|---|---|
| Spacegroup | I 1 2 1 | a: 127.250Å b: 76.030Å c: 300.267Å | α: 90.00° β: 92.21° γ: 90.00° | ||
| Resolution | 2.36 Å | Reflections | 118259 | Test set | 5970 (5.0%) |
| R | 0.1710 | R-free | 0.2180 | ||
| According to PDB-REDO | |||||
| Resolution | 2.36 Å | Reflections | 118259 | Test set | 5970 (5.0%) |
| Twin | false | Radiation damage | 87 | ||
| 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 | 0.1752 | 0.1653 |
| R-free | 0.2201 | 0.1973 |
| Bond length RMS Z-score | 0.794 | 0.355 |
| Bond angle RMS Z-score | 0.674 | 0.543 |
| Model quality | ||
| Ramachandran plot normality | -1.845 34 | -1.913 33 |
| Rotamer normality | -1.416 63 | -1.815 55 |
| Coarse packing | N/A N/A | N/A N/A |
| Fine packing | N/A N/A | N/A N/A |
| MolProbity Clashscore | 5.940 45 | 2.680 79 |
| Hydrogen bond satisfaction | N/A N/A | N/A N/A |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | N/A |
| Side chains built | 0 |
| Waters removed | N/A |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 58 |
| Residues fitting density worse | 2 |