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Structure of a Streptococcus pneumoniae fucose binding module in complex with the Lewis Y antigen |
This entry was created with PDB-REDO version 7.32. |
From original header | |||||||
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Spacegroup | P 21 21 21 | a: 43.707 Å | b: 59.943 Å | c: 98.889 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 1.60 Å | Reflections | 34122 | Test set | 1687 (4.9%) | ||
R | 0.1480 | R-free | 0.2090 | ||||
According to PDB-REDO | |||||||
Resolution | 1.60 Å | Reflections | 34122 | Test set | 1687 (4.9%) | ||
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 | 0.1645 | 0.1752 |
R-free | 0.2149 | 0.2107 |
Bond length RMS Z-score | 0.775 | 0.444 |
Bond angle RMS Z-score | 0.828 | 0.683 |
Model quality | ||
Ramachandran plot normality | -0.042 79 | 0.337 87 |
Rotamer normality | -0.093 91 | 0.828 98 |
Coarse packing | 0.449 81 | 0.503 83 |
Fine packing | -1.165 46 | -0.822 60 |
Bump severity | 0.066 15 | 0.103 10 |
Hydrogen bond satisfaction | 0.892 40 | 0.879 28 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 9 |
Side chains flipped | 0 |
Waters removed | 53 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 7 |
Residues fitting density worse | 0 |