SrpA adhesin in complex with the Neu5Ac-galactoside disaccharide |
This entry was created with PDB-REDO version 8.06. |
From original header | |||||||
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Spacegroup | C 1 2 1 | a: 174.522 Å | b: 46.769 Å | c: 46.769 Å | α: 90.00° | β: 102.72° | γ: 90.00° |
Resolution | 1.89 Å | Reflections | 40927 | Test set | 2059 (5.0%) | ||
R | 0.1767 | R-free | 0.2010 | ||||
According to PDB-REDO | |||||||
Resolution | 1.89 Å | Reflections | 40927 | Test set | 2059 (5.0%) | ||
Twin | false | Radiation damage | 74 | ||||
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 | 0.1843 | 0.1695 |
R-free | 0.2168 R-free was considered biased, the estimated unbiased R-free was used | 0.2094 |
Bond length RMS Z-score | 0.515 | 0.320 |
Bond angle RMS Z-score | 0.640 | 0.511 |
Model quality | ||
Ramachandran plot normality | 0.322 88 | 0.556 91 |
Rotamer normality | -0.753 77 | 0.411 94 |
Coarse packing | 0.342 64 | 0.384 66 |
Fine packing | -1.401 36 | -1.227 44 |
Bump severity | 0.010 56 | 0.000 95 |
Hydrogen bond satisfaction | 0.910 64 | 0.879 28 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 3 |
Side chains flipped | 0 |
Waters removed | 89 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 9 |
Residues fitting density worse | 0 |