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| Structure of histone demethylase REF6 complexed with DNA |
| This entry was created with PDB-REDO version 8.07. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 32 2 1 | a: 96.087 Å | b: 96.087 Å | c: 96.087 Å | α: 90.00° | β: 90.00° | γ: 120.00° |
| Resolution | 2.70 Å | Reflections | 11112 | Test set | 596 (5.4%) | ||
| R | 0.2211 | R-free | 0.2566 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.70 Å | Reflections | 11112 | Test set | 596 (5.4%) | ||
| Twin | false | Radiation damage |
96
Data shows severe radiation damage
|
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| PDB-REDO files | |||||||
| Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
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| Links | |||||||
| PDBe | RCSB PDB | 3D bionotes | Proteopedia | ||||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.2233 | 0.1831 |
| R-free | 0.2558 | 0.2348 |
| Bond length RMS Z-score | 0.942 | 0.612 |
| Bond angle RMS Z-score | 0.772 | 0.986 |
| Model quality | ||
| Ramachandran plot normality | -3.456 13 | -3.851 10 |
| Rotamer normality | -4.244 16 | -4.403 14 |
| Coarse packing | N/A N/A | -2.783 1 |
| Fine packing | N/A N/A | -4.128 0 |
| Dinucleotide conformation (CONFAL) | 68.8 91 | 60.9 80 |
| Base pair conformation | 1.2 81 | 1.0 89 |
| Bump severity | 0.036 23 | 0.088 11 |
| Hydrogen bond satisfaction | 0.699 2 | 0.705 2 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 1 |
| Side chains flipped | 25 |
| Waters removed | 5 |
| Peptides flipped | 2 |
| Chiralities fixed | 0 |
| Residues fitting density better | 22 |
| Residues fitting density worse | 0 |