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Crystal structure of the Staphylococcal superantigen-like protein SSL5 in complex with sialyl-Lewis X at pH 7.4 |
This entry was created with PDB-REDO version 8.04. |
From original header | |||||||
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Spacegroup | P 43 21 2 | a: 52.223 Å | b: 52.223 Å | c: 236.657 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 2.75 Å | Reflections | 9228 | Test set | 0 (0.0%) | ||
R | 0.2095 | R-free | 0.2686 | ||||
According to PDB-REDO | |||||||
Resolution | 2.75 Å | Reflections | 9228 | Test set | 979 (10.6%) New test set, PDB-REDO compensated for this | ||
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 | |
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Crystallographic refinement | ||
R | 0.2113 | 0.2170 |
R-free | 0.2547 R-free was considered biased, the estimated unbiased R-free was used | 0.2540 |
Bond length RMS Z-score | 1.189 | 0.200 |
Bond angle RMS Z-score | 0.975 | 0.424 |
Model quality | ||
Ramachandran plot normality | -4.149 8 | -3.031 16 |
Rotamer normality | -3.765 29 | -0.239 89 |
Coarse packing | -0.979 17 | -0.700 27 |
Fine packing | -1.188 45 | -0.797 61 |
Bump severity | 0.161 7 | 0.091 11 |
Hydrogen bond satisfaction | 0.913 68 | 0.887 35 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 4 |
Side chains flipped | 0 |
Waters removed | 3 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 0 |