| AS-isolated hybrid cluster protein from Desulfovibrio vulgaris X-ray structure at 1.35A resolution using iron anomalous signal |
| This entry was created with PDB-REDO version 8.22 using the deposited PDB model version 2.0 |
| From original header | |||||
|---|---|---|---|---|---|
| Spacegroup | P 21 21 21 | a: 64.270Å b: 66.843Å c: 134.764Å | α: 90.00° β: 90.00° γ: 90.00° | ||
| Resolution | 1.35 Å | Reflections | 127874 | Test set | 6423 (5.0%) |
| R | 0.1280 | R-free | 0.1770 | ||
| According to PDB-REDO | |||||
| Resolution | 1.35 Å | Reflections | 127874 | Test set | 6423 (5.0%) |
| Twin | false | Radiation damage | 89 | ||
| 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 | 0.1167 | 0.1088 |
| R-free | 0.1523 | 0.1374 |
| Bond length RMS Z-score | 1.061 | 0.737 |
| Bond angle RMS Z-score | 1.246 | 0.779 |
| Model quality | ||
| Ramachandran plot normality | 0.224 86 | 0.505 90 |
| Rotamer normality | 0.488 95 | 1.274 99 |
| Coarse packing | 1.582 94 | 1.510 93 |
| Fine packing | 0.663 92 | 0.704 93 |
| MolProbity Clashscore | 3.030 75 | 1.280 94 |
| Hydrogen bond satisfaction | 0.897 46 | 0.899 49 |
| 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 | 30 |
| Residues fitting density worse | 4 |