| The crystal structure of the Hybrid Cluster Protein from Desulfovibrio desulfuricans containing molecules in the oxidized and reduced states. |
| 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: 57.300Å b: 61.200Å c: 72.000Å | α: 82.80° β: 73.70° γ: 87.30° | ||
| Resolution | 1.25 Å | Reflections | 229273 | Test set | 0 (0.0%) |
| R | 0.1400 | R-free | 0.1530 | ||
| According to PDB-REDO | |||||
| Resolution | 1.25 Å | Reflections | 229273 | Test set |
11475 (5.0%)
New test set, PDB-REDO compensated for this
|
| Twin | false | Radiation damage |
99
Data shows severe radiation damage
|
||
| 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 | 0.1415 | 0.1031 |
| R-free |
0.1752
R-free was considered biased, the
estimated unbiased R-free was used
|
0.1299 |
| Bond length RMS Z-score | 0.830 | 0.750 |
| Bond angle RMS Z-score | 0.893 | 0.835 |
| Model quality | ||
| Ramachandran plot normality | 0.207 86 | 0.176 85 |
| Rotamer normality | 0.180 92 | 0.860 97 |
| Coarse packing | 1.705 95 | 1.741 95 |
| Fine packing | 2.116 98 | 2.156 98 |
| MolProbity Clashscore | 3.180 73 | 3.360 71 |
| Hydrogen bond satisfaction | 0.886 34 | 0.889 37 |
| 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 | 440 |
| Residues fitting density worse | 1 |