| REDUCED HYBRID CLUSTER PROTEIN FROM DESULFOVIBRIO DESULFURICANS X-RAY STRUCTURE AT 1.25A RESOLUTION |
| This entry was created with PDB-REDO version 8.22 using the deposited PDB model version 1.6 |
| From original header | |||||
|---|---|---|---|---|---|
| Spacegroup | P 1 | a: 57.750Å b: 61.990Å c: 72.800Å | α: 82.72° β: 73.74° γ: 87.44° | ||
| Resolution | 1.25 Å | Reflections | 246618 | Test set | 6123 (2.5%) |
| R | 0.1331 | R-free | 0.1504 | ||
| According to PDB-REDO | |||||
| Resolution | 1.25 Å | Reflections | 246618 | Test set | 6123 (2.5%) |
| Twin | false | Radiation damage | 88 | ||
| 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 | 0.1337 | 0.0918 |
| R-free | 0.1516 | 0.1150 |
| Bond length RMS Z-score | 0.828 | 0.605 |
| Bond angle RMS Z-score | 0.885 | 0.768 |
| Model quality | ||
| Ramachandran plot normality | 0.200 86 | 0.233 86 |
| Rotamer normality | 0.210 92 | 0.962 97 |
| Coarse packing | 1.246 90 | 1.337 91 |
| Fine packing | 1.813 98 | 1.943 98 |
| MolProbity Clashscore | 3.070 74 | 2.300 84 |
| Hydrogen bond satisfaction | 0.894 42 | 0.894 42 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | N/A |
| Side chains built | 4 |
| Waters removed | N/A |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 484 |
| Residues fitting density worse | 0 |