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| E. coli methionine aminopeptidase Mn-form with inhibitor A04 |
| This entry was created with PDB-REDO version 8.01 using the deposited PDB model version 1.2 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 1 21 1 | a: 38.199 Å | b: 60.605 Å | c: 50.624 Å | α: 90.00° | β: 104.80° | γ: 90.00° |
| Resolution | 1.63 Å | Reflections | 27702 | Test set | 2758 (10%) | ||
| R | 0.2130 | R-free | 0.2380 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.63 Å | Reflections | 27702 | Test set | 2758 (10%) | ||
| Twin | false | Radiation damage | N/A | ||||
| 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 | 0.2049 | 0.1774 |
| R-free | 0.2305 | 0.2026 |
| Bond length RMS Z-score | 0.259 | 0.515 |
| Bond angle RMS Z-score | 0.639 | 0.768 |
| Model quality | ||
| Ramachandran plot normality | -0.328 72 | -0.177 76 |
| Rotamer normality | -1.365 70 | -0.470 86 |
| Coarse packing | 0.658 87 | 0.715 89 |
| Fine packing | 2.116 98 | 2.183 98 |
| Bump severity | 0.006 70 | 0.021 38 |
| Hydrogen bond satisfaction | 0.872 23 | 0.885 33 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 4 |
| Side chains built | 0 |
| Waters removed | 8 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 7 |
| Residues fitting density worse | 0 |