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| CRYSTAL STRUCTURES OF THE CHROMOSOMAL PROTEINS SSO7D/SAC7D BOUND TO DNA CONTAINING T-G MISMATCHED BASE PAIRS |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 1.4 |
| From original header | |||||
|---|---|---|---|---|---|
| Spacegroup | P 21 21 21 | a: 47.475Å b: 49.800Å c: 37.681Å | α: 90.00° β: 90.00° γ: 90.00° | ||
| Resolution | 1.45 Å | Reflections | 14744 | Test set | 0 (0.0%) |
| R | 0.2290 | R-free | 0.2868 | ||
| According to PDB-REDO | |||||
| Resolution | 1.45 Å | Reflections | 14744 | Test set |
831 (5.6%)
New test set, PDB-REDO compensated for this
|
| Twin | false | Radiation damage | 63 | ||
| 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 | 0.3065 | 0.1996 |
| R-free |
0.2395
R-free was considered biased, the
estimated unbiased R-free was used
|
0.2317 |
| Bond length RMS Z-score | 19.271 | 0.462 |
| Bond angle RMS Z-score | 4.030 | 0.800 |
| Model quality | ||
| Ramachandran plot normality | -0.290 75 | 0.008 82 |
| Rotamer normality | -5.604 6 | -3.447 25 |
| Coarse packing | -1.110 9 | -1.039 11 |
| Fine packing | -3.249 1 | -2.817 3 |
| Dinucleotide conformation (CONFAL) | 55.1 74 | 57.5 78 |
| Base pair conformation | 0.8 96 | 0.7 98 |
| Bump severity | 0.008 62 | 0.007 65 |
| Hydrogen bond satisfaction | 0.737 2 | 0.752 3 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 1 |
| Side chains built | 0 |
| Waters removed | 28 |
| Peptides flipped | 2 |
| Chiralities fixed | 0 |
| Residues fitting density better | 10 |
| Residues fitting density worse | 0 |