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| Crystal Structure of apo HydF from thermotoga maritima |
| This entry was created with PDB-REDO version 8.13 using Foldit model 2014039 from player LociOiling |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | I 4 | a: 126.140 Å | b: 126.140 Å | c: 68.840 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
| Resolution | 3.00 Å | Reflections | 10683 | Test set | 1050 (9.8%) | ||
| R | 0.2440 | R-free | 0.2800 | ||||
| According to PDB-REDO | |||||||
| Resolution | 3.00 Å | Reflections | 10683 | Test set | 1050 (9.8%) | ||
| Twin | false | Radiation damage | 92 | ||||
| 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 | 0.2702 | 0.2270 |
| R-free | 0.3116 | 0.3076 |
| Bond length RMS Z-score | 0.941 | 0.524 |
| Bond angle RMS Z-score | 0.880 | 0.783 |
| Model quality | ||
| Ramachandran plot normality | -4.337 7 | -5.663 3 |
| Rotamer normality | -5.866 5 | -6.088 4 |
| Coarse packing | -1.174 8 | -1.018 11 |
| Fine packing | -2.657 4 | -2.458 6 |
| Bump severity | 0.059 15 | 0.142 7 |
| Hydrogen bond satisfaction | 0.834 10 | 0.799 5 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 1 |
| Side chains built | 0 |
| Waters removed | 0 |
| Peptides flipped | 16 |
| Chiralities fixed | 0 |
| Residues fitting density better | 2 |
| Residues fitting density worse | 0 |