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Crystal structure of mouse Peptide N-Glycanase C-terminal domain in complex with mannopentaose |
This entry was created with PDB-REDO version 8.01. |
From original header | |||||||
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Spacegroup | P 1 21 1 | a: 45.706 Å | b: 41.646 Å | c: 94.900 Å | α: 90.00° | β: 94.89° | γ: 90.00° |
Resolution | 1.75 Å | Reflections | 35877 | Test set | 1857 (5.2%) | ||
R | 0.1720 | R-free | 0.2080 | ||||
According to PDB-REDO | |||||||
Resolution | 1.75 Å | Reflections | 35877 | Test set | 1857 (5.2%) | ||
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 | 0.1777 | 0.1768 |
R-free | 0.2129 | 0.2127 |
Bond length RMS Z-score | 0.633 | 0.369 |
Bond angle RMS Z-score | 0.746 | 0.661 |
Model quality | ||
Ramachandran plot normality | -0.458 69 | 0.146 83 |
Rotamer normality | -1.184 74 | 0.006 92 |
Coarse packing | 1.369 97 | 1.264 96 |
Fine packing | -1.029 52 | -1.144 47 |
Bump severity | 0.021 38 | 0.001 92 |
Hydrogen bond satisfaction | 0.941 94 | 0.932 88 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 7 |
Side chains flipped | 3 |
Waters removed | 8 |
Peptides flipped | 1 |
Chiralities fixed | 0 |
Residues fitting density better | 1 |
Residues fitting density worse | 1 |