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Raffinose and panose binding protein from Bifidobacterium animalis subsp. lactis Bl-04, bound with raffinose, selenomethionine derivative |
This entry was created with PDB-REDO version 7.32. |
From original header | |||||||
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Spacegroup | P 21 21 21 | a: 55.385 Å | b: 90.949 Å | c: 145.530 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 2.02 Å | Reflections | 48998 | Test set | 2450 (5.0%) | ||
R | 0.1690 | R-free | 0.2100 | ||||
According to PDB-REDO | |||||||
Resolution | 2.02 Å | Reflections | 48998 | Test set | 2450 (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 | 0.1755 | 0.1619 |
R-free | 0.2168 | 0.2168 |
Bond length RMS Z-score | 0.523 | 0.541 |
Bond angle RMS Z-score | 0.624 | 0.687 |
Model quality | ||
Ramachandran plot normality | -0.155 77 | 0.012 80 |
Rotamer normality | -0.218 90 | -0.403 87 |
Coarse packing | 0.299 76 | 0.359 78 |
Fine packing | -1.537 30 | -1.484 32 |
Bump severity | 0.060 16 | 0.060 16 |
Hydrogen bond satisfaction | 0.879 28 | 0.892 40 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 14 |
Side chains flipped | 0 |
Waters removed | 38 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 0 |