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Crystal Structure of P Domain from Norwalk Virus Strain Vietnam 026 in complex with HBGA type H2 (diglycan) |
This entry was created with PDB-REDO version 8.01. |
From original header | |||||||
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Spacegroup | P 1 21 1 | a: 65.117 Å | b: 78.768 Å | c: 69.490 Å | α: 90.00° | β: 99.93° | γ: 90.00° |
Resolution | 1.25 Å | Reflections | 189903 | Test set | 9549 (5.0%) | ||
R | 0.1682 | R-free | 0.1820 | ||||
According to PDB-REDO | |||||||
Resolution | 1.25 Å | Reflections | 189903 | Test set | 9549 (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 | 0.1608 | 0.1357 |
R-free | 0.1760 | 0.1585 |
Bond length RMS Z-score | 0.770 | 0.489 |
Bond angle RMS Z-score | 0.870 | 0.773 |
Model quality | ||
Ramachandran plot normality | -0.333 72 | 0.049 81 |
Rotamer normality | 0.707 97 | 1.337 99 |
Coarse packing | -0.902 19 | -0.925 18 |
Fine packing | -1.646 26 | -1.382 37 |
Bump severity | 0.009 61 | 0.007 67 |
Hydrogen bond satisfaction | 0.890 38 | 0.891 39 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 7 |
Side chains flipped | 0 |
Waters removed | 136 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 119 |
Residues fitting density worse | 0 |