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Structure of a Streptococcus pneumoniae fucose binding module in complex with fucose |
This entry was created with PDB-REDO version 7.32. |
From original header | |||||||
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Spacegroup | P 21 21 21 | a: 43.523 Å | b: 60.771 Å | c: 99.499 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 1.50 Å | Reflections | 40044 | Test set | 2014 (5.0%) | ||
R | 0.1550 | R-free | 0.1920 | ||||
According to PDB-REDO | |||||||
Resolution | 1.50 Å | Reflections | 40044 | Test set | 2014 (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 | 0.1643 | 0.1718 |
R-free | 0.2011 | 0.1973 |
Bond length RMS Z-score | 0.741 | 0.399 |
Bond angle RMS Z-score | 0.816 | 0.646 |
Model quality | ||
Ramachandran plot normality | 0.016 80 | 0.208 84 |
Rotamer normality | -0.374 88 | 0.848 98 |
Coarse packing | 0.475 82 | 0.524 84 |
Fine packing | -1.263 42 | -0.884 58 |
Bump severity | 0.000 96 | 0.000 96 |
Hydrogen bond satisfaction | 0.882 30 | 0.864 19 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 10 |
Side chains flipped | 0 |
Waters removed | 89 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 5 |
Residues fitting density worse | 2 |