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| Crystal structure of ScGas2 in complex with compound 9 |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 2.2 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 21 21 21 | a: 50.200 Å | b: 71.200 Å | c: 150.440 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
| Resolution | 1.70 Å | Reflections | 59931 | Test set | 1832 (3.1%) | ||
| R | 0.1954 | R-free | 0.2119 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.70 Å | Reflections | 59931 | Test set |
1831 (3.1%)
New test set, PDB-REDO compensated for this
|
||
| Twin | false | Radiation damage | 61 | ||||
| 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 | 0.1975 | 0.1666 |
| R-free |
0.2278
R-free was considered biased, the
estimated unbiased R-free was used
|
0.1921 |
| Bond length RMS Z-score | 0.810 | 0.258 |
| Bond angle RMS Z-score | 0.794 | 0.533 |
| Model quality | ||
| Ramachandran plot normality | -0.793 61 | -0.585 67 |
| Rotamer normality | -0.524 81 | -0.210 87 |
| Coarse packing | 0.312 63 | 0.404 67 |
| Fine packing | -0.913 57 | -0.926 56 |
| Bump severity | 0.000 95 | 0.001 90 |
| Hydrogen bond satisfaction | 0.879 28 | 0.874 24 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 4 |
| Side chains built | 0 |
| Waters removed | 10 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 68 |
| Residues fitting density worse | 0 |