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Raffinose and panose binding protein from Bifidobacterium animalis subsp. lactis Bl-04, bound with raffinose |
This entry was created with PDB-REDO version 7.32. |
From original header | |||||||
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Spacegroup | P 21 21 21 | a: 55.540 Å | b: 90.820 Å | c: 146.750 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 1.37 Å | Reflections | 150939 | Test set | 7588 (5.0%) | ||
R | 0.1320 | R-free | 0.1670 | ||||
According to PDB-REDO | |||||||
Resolution | 1.37 Å | Reflections | 150939 | Test set | 7584 (5.0%) 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 | |
---|---|---|
Crystallographic refinement | ||
R | 0.1380 | 0.1254 |
R-free | 0.1720 R-free was considered biased, the estimated unbiased R-free was used | 0.1609 |
Bond length RMS Z-score | 0.566 | 0.671 |
Bond angle RMS Z-score | 0.680 | 0.801 |
Model quality | ||
Ramachandran plot normality | 0.742 92 | 1.240 96 |
Rotamer normality | 0.930 98 | 0.784 97 |
Coarse packing | 0.830 91 | 0.809 91 |
Fine packing | -0.935 56 | -0.819 60 |
Bump severity | 0.046 20 | 0.054 18 |
Hydrogen bond satisfaction | 0.888 36 | 0.902 53 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 13 |
Side chains flipped | 0 |
Waters removed | 188 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 24 |
Residues fitting density worse | 0 |