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SpAga D472N structure in complex with raffinose |
This entry was created with PDB-REDO version 8.04. |
From original header | |||||||
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Spacegroup | I 2 2 2 | a: 91.027 Å | b: 127.452 Å | c: 151.955 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 2.00 Å | Reflections | 56451 | Test set | 2837 (5.0%) | ||
R | 0.1908 | R-free | 0.2317 | ||||
According to PDB-REDO | |||||||
Resolution | 2.00 Å | Reflections | 56451 | Test set | 2837 (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 | 0.1885 | 0.1845 |
R-free | 0.2262 | 0.2155 |
Bond length RMS Z-score | 0.468 | 0.525 |
Bond angle RMS Z-score | 0.781 | 0.680 |
Model quality | ||
Ramachandran plot normality | -1.233 47 | -1.309 45 |
Rotamer normality | -1.169 74 | -0.685 83 |
Coarse packing | 0.516 83 | 0.483 82 |
Fine packing | -1.272 41 | -1.239 43 |
Bump severity | 0.025 34 | 0.027 32 |
Hydrogen bond satisfaction | 0.897 46 | 0.904 56 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 15 |
Side chains flipped | 7 |
Waters removed | 10 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 0 |