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| Poliovirus polymerase elongation complex with 2',3'-dideoxy-ctp |
| This entry was created with PDB-REDO version 8.01 using the deposited PDB model version 1.3 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 1 | a: 60.528 Å | b: 60.539 Å | c: 192.936 Å | α: 83.82° | β: 83.84° | γ: 77.35° |
| Resolution | 2.41 Å | Reflections | 132261 | Test set | 7555 (5.7%) | ||
| R | 0.2173 | R-free | 0.2613 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.19 Å | Reflections | 132261 | Test set |
6679 (5.0%)
New test set, PDB-REDO compensated for this
|
||
| Twin | false | Radiation damage | N/A | ||||
| 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 | 0.3109 | 0.2477 |
| R-free |
0.3716
R-free was considered biased, the
estimated unbiased R-free was used
|
0.2902 |
| Bond length RMS Z-score | 0.469 | 0.501 |
| Bond angle RMS Z-score | 0.695 | 0.811 |
| Model quality | ||
| Ramachandran plot normality | -2.284 25 | -1.459 41 |
| Rotamer normality | -3.607 31 | -1.954 59 |
| Coarse packing | 0.128 68 | 0.034 64 |
| Fine packing | -1.900 17 | -1.751 22 |
| Dinucleotide conformation (CONFAL) | 68.7 91 | 66.7 89 |
| Base pair conformation | 2.6 27 | 1.2 78 |
| Bump severity | 0.024 35 | 0.036 25 |
| Hydrogen bond satisfaction | 0.824 8 | 0.825 8 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 17 |
| Side chains flipped | 0 |
| Waters removed | 348 |
| Peptides flipped | 7 |
| Chiralities fixed | 0 |
| Residues fitting density better | 30 |
| Residues fitting density worse | 17 |