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Structure of the P domain from a GI.7 Norovirus variant in complex with H-type 2 HBGA |
This entry was created with PDB-REDO version 8.03. |
From original header | |||||||
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Spacegroup | P 1 | a: 62.398 Å | b: 63.150 Å | c: 90.320 Å | α: 72.71° | β: 82.24° | γ: 60.75° |
Resolution | 1.55 Å | Reflections | 161298 | Test set | 8109 (5.0%) | ||
R | 0.1542 | R-free | 0.1727 | ||||
According to PDB-REDO | |||||||
Resolution | 1.55 Å | Reflections | 161298 | Test set | 8109 (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 | 0.1607 | 0.1646 |
R-free | 0.1747 | 0.1820 |
Bond length RMS Z-score | 0.671 | 0.503 |
Bond angle RMS Z-score | 0.822 | 0.676 |
Model quality | ||
Ramachandran plot normality | 0.003 80 | 0.004 80 |
Rotamer normality | 1.100 98 | 0.734 97 |
Coarse packing | -1.042 15 | -1.050 15 |
Fine packing | -1.516 31 | -1.263 42 |
Bump severity | 0.007 67 | 0.001 92 |
Hydrogen bond satisfaction | 0.882 30 | 0.887 35 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 27 |
Side chains flipped | 6 |
Waters removed | 179 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 12 |
Residues fitting density worse | 0 |