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| Crystal structure of human ALKBH3 bound to 3mC containing ssDNA through distal crosslink |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 1.3 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 1 21 1 | a: 108.615 Å | b: 142.171 Å | c: 130.110 Å | α: 90.00° | β: 113.07° | γ: 90.00° |
| Resolution | 3.66 Å | Reflections | 35566 | Test set | 796 (2.2%) | ||
| R | 0.2270 | R-free | 0.2730 | ||||
| According to PDB-REDO | |||||||
| Resolution | 3.66 Å | Reflections | 35566 | Test set | 796 (2.2%) | ||
| Twin | false | Radiation damage | 92 | ||||
| PDB-REDO files | |||||||
| Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
|||||
| Links | |||||||
| PDBe | RCSB PDB | 3D bionotes | Proteopedia | ||||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.2504 | 0.2267 |
| R-free |
0.3054
R-free was considered biased, the
estimated unbiased R-free was used
|
0.2505 |
| Bond length RMS Z-score | 1.257 | 0.230 |
| Bond angle RMS Z-score | 0.693 | 0.431 |
| Model quality | ||
| Ramachandran plot normality | -1.065 54 | -1.519 42 |
| Rotamer normality | -1.189 68 | -1.788 55 |
| Coarse packing | -0.595 23 | -0.262 37 |
| Fine packing | -0.257 77 | 0.127 85 |
| Dinucleotide conformation (CONFAL) | 0.0 3 | 0.0 3 |
| Base pair conformation | N/A N/A | N/A N/A |
| Bump severity | 0.033 25 | 0.010 56 |
| Hydrogen bond satisfaction | 0.713 2 | 0.605 0 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 10 |
| Side chains built | 0 |
| Waters removed | 0 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 7 |
| Residues fitting density worse | 0 |