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| Crystal structure of MBTD1 YY1 complex |
| This entry was created with PDB-REDO version 8.04 using the deposited PDB model version 1.1 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 21 21 21 | a: 70.360 Å | b: 104.710 Å | c: 135.520 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
| Resolution | 2.59 Å | Reflections | 31789 | Test set | 1590 (5.0%) | ||
| R | 0.2129 | R-free | 0.2332 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.59 Å | Reflections | 31789 | Test set | 1590 (5.0%) | ||
| Twin | false | Radiation damage | N/A | ||||
| 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 | 0.2348 | 0.2249 |
| R-free | 0.2529 | 0.2606 |
| Bond length RMS Z-score | 0.577 | 0.271 |
| Bond angle RMS Z-score | 0.708 | 0.563 |
| Model quality | ||
| Ramachandran plot normality | -1.557 41 | -1.838 34 |
| Rotamer normality | -0.600 80 | -1.642 58 |
| Coarse packing | N/A N/A | N/A N/A |
| Fine packing | N/A N/A | N/A N/A |
| Bump severity | 0.000 95 | 0.000 95 |
| Hydrogen bond satisfaction | N/A N/A | N/A N/A |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 11 |
| Side chains built | 11 |
| Waters removed | 1 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |