This is an obsolete entry, it comes from attic cc472422e.
| 2.3 ANGSTROM STRUCTURE OF PHOSPHODIESTERASE TREATED VIVID |
| This entry was created with PDB-REDO version 7.00. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 1 21 1 | a: 64.120 Å | b: 80.570 Å | c: 64.110 Å | α: 90.00° | β: 90.02° | γ: 90.00° |
| Resolution | 2.20 Å | Reflections | 33147 | Test set | 2897 (8.7%) | ||
| R | 0.2340 | R-free | 0.2660 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.20 Å | Reflections | 33147 | Test set | 2897 (8.7%) | ||
| 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 | 0.3024 | 0.1745 |
| R-free |
0.3142
R-free was considered biased, the
estimated unbiased R-free was used
|
0.2168 |
| Bond length RMS Z-score | 0.352 | 0.566 |
| Bond angle RMS Z-score | 0.589 | 0.756 |
| Model quality | ||
| Ramachandran plot normality | -2.235 19 | 0.547 88 |
| Rotamer normality | -4.252 8 | -1.800 45 |
| Coarse packing | -1.220 N/A | -0.667 N/A |
| Fine packing | -1.751 17 | -0.806 61 |
| Bump severity | 0.044 31 | 0.012 75 |
| Hydrogen bond satisfaction | 0.910 62 | 0.922 78 |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 9 |
| Side chains flipped | 0 |
| Waters removed | 143 |
| Peptides flipped | 1 |
| Chiralities fixed | 0 |
| Residues fitting density better | 362 |
| Residues fitting density worse | 0 |