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Structure of the catalytic domain of Aspergillus niger Glucoamylase |
This entry was created with PDB-REDO version 8.04. |
From original header | |||||||
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Spacegroup | P 21 21 21 | a: 56.369 Å | b: 73.125 Å | c: 102.880 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 2.30 Å | Reflections | 19408 | Test set | 972 (5.0%) | ||
R | 0.2509 | R-free | 0.3433 | ||||
According to PDB-REDO | |||||||
Resolution | 2.30 Å | Reflections | 19408 | Test set | 972 (5.0%) | ||
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 | 0.2510 | 0.2559 |
R-free | 0.3438 | 0.3105 |
Bond length RMS Z-score | 0.851 | 0.185 |
Bond angle RMS Z-score | 0.681 | 0.394 |
Model quality | ||
Ramachandran plot normality | -4.028 9 | -3.468 13 |
Rotamer normality | -4.432 14 | -2.815 35 |
Coarse packing | N/A N/A | N/A N/A |
Fine packing | N/A N/A | N/A N/A |
Bump severity | 0.000 95 | 0.000 95 |
Hydrogen bond satisfaction | N/A N/A | N/A N/A |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 5 |
Side chains flipped | 0 |
Waters removed | 5 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 0 |