| Crystal Structure of Native S195A Thrombin with an Unoccupied Active Site |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 2.3 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 1 21 1 | a: 71.230 Å | b: 76.580 Å | c: 97.320 Å | α: 90.00° | β: 106.64° | γ: 90.00° |
| Resolution | 1.80 Å | Reflections | 91794 | Test set | 1000 (1.1%) | ||
| R | 0.2220 | R-free | 0.2450 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.80 Å | Reflections | 91794 | Test set | 1000 (1.1%) | ||
| Twin | false | Radiation damage | 25 | ||||
| PDB-REDO files | |||||||
| Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
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| Links | |||||||
| PDBe | RCSB PDB | 3D bionotes | Proteopedia | ||||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.2172 | 0.1876 |
| R-free | 0.2383 | 0.2176 |
| Bond length RMS Z-score | 0.551 | 0.705 |
| Bond angle RMS Z-score | 0.753 | 0.801 |
| Model quality | ||
| Ramachandran plot normality | -2.574 22 | -1.198 50 |
| Rotamer normality | -1.806 55 | -1.185 68 |
| Coarse packing | -0.984 12 | -0.774 17 |
| Fine packing | 1.612 97 | 1.892 98 |
| Bump severity | 0.136 8 | 0.122 8 |
| Hydrogen bond satisfaction | 0.878 27 | 0.887 35 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 17 |
| Side chains flipped | 0 |
| Waters removed | 18 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 137 |
| Residues fitting density worse | 0 |