| Crystal structure of the di-tetraheme cytochrome c3 from Desulfovibrio gigas at 1.2 Angstrom resolution |
| This entry was created with PDB-REDO version 8.22 using the deposited PDB model version 2.0 |
| From original header | |||||
|---|---|---|---|---|---|
| Spacegroup | P 31 | a: 56.670Å b: 56.670Å c: 94.170Å | α: 90.00° β: 90.00° γ: 120.00° | ||
| Resolution | 1.20 Å | Reflections | 101181 | Test set | 0 (0.0%) |
| R | 0.1303 | R-free | 0.1568 | ||
| According to PDB-REDO | |||||
| Resolution | 1.20 Å | Reflections | 101181 | Test set |
5283 (5.2%)
New test set, PDB-REDO compensated for this
|
| Twin | false | Radiation damage | 39 | ||
| PDB-REDO files | |||||
| Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
|||
| Links | |||||
| PDBe | RCSB PDB | Proteopedia | |||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.1179 | 0.1263 |
| R-free |
0.1354
R-free was considered biased, the
estimated unbiased R-free was used
|
0.1435 |
| Bond length RMS Z-score | 1.404 | 0.954 |
| Bond angle RMS Z-score | 1.503 | 0.935 |
| Model quality | ||
| Ramachandran plot normality | -1.296 47 | -1.176 51 |
| Rotamer normality | -0.081 89 | 0.801 97 |
| Coarse packing | -3.325 0 | -3.369 0 |
| Fine packing | -2.230 9 | -2.211 10 |
| MolProbity Clashscore | 2.020 87 | 4.040 63 |
| Hydrogen bond satisfaction | 0.898 47 | 0.892 40 |
| WHAT_CHECK | Report | Report |
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 | 1 |
| Residues fitting density worse | 12 |