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| The crystal structure of a DNA:RNA hybrid duplex sequence CTTTTCTTTG containing an LNA-Amide-LNA modification |
| This entry was created with PDB-REDO version 8.04 using the deposited PDB model version 2.1 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 32 2 1 | a: 49.150 Å | b: 49.150 Å | c: 90.960 Å | α: 90.00° | β: 90.00° | γ: 120.00° |
| Resolution | 2.57 Å | Reflections | 4364 | Test set | 0 (0.0%) | ||
| R | 0.2326 | R-free | 0.2513 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.57 Å | Reflections | 4364 | Test set |
434 (9.9%)
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 | 0.2472 | 0.2311 |
| R-free |
0.2979
R-free was considered biased, the
estimated unbiased R-free was used
|
0.2695 |
| Bond length RMS Z-score | 1.086 | 0.324 |
| Bond angle RMS Z-score | 1.198 | 0.634 |
| Model quality | ||
| Coarse packing | N/A N/A | N/A N/A |
| Fine packing | N/A N/A | N/A N/A |
| Dinucleotide conformation (CONFAL) | 74.7 95 | 76.4 96 |
| Base pair conformation | 3.1 19 | 2.3 37 |
| 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 | 0 |
| Side chains built | 0 |
| Waters removed | 0 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 1 |
| Residues fitting density worse | 0 |