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Crystal Structure of P Domain from Norwalk Virus Strain Vietnam 026 in complex with HBGA type A |
This entry was created with PDB-REDO version 8.01. |
From original header | |||||||
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Spacegroup | P 1 21 1 | a: 65.194 Å | b: 78.987 Å | c: 70.100 Å | α: 90.00° | β: 101.06° | γ: 90.00° |
Resolution | 1.48 Å | Reflections | 115772 | Test set | 5835 (5.0%) | ||
R | 0.1776 | R-free | 0.1982 | ||||
According to PDB-REDO | |||||||
Resolution | 1.48 Å | Reflections | 115772 | Test set | 5835 (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 | 0.1703 | 0.1499 |
R-free | 0.1876 | 0.1807 |
Bond length RMS Z-score | 0.372 | 0.402 |
Bond angle RMS Z-score | 0.578 | 0.668 |
Model quality | ||
Ramachandran plot normality | -0.270 74 | -0.254 74 |
Rotamer normality | 0.707 97 | 1.080 98 |
Coarse packing | -1.053 14 | -1.068 14 |
Fine packing | -1.804 20 | -1.661 25 |
Bump severity | 0.006 70 | 0.005 74 |
Hydrogen bond satisfaction | 0.893 41 | 0.891 39 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 7 |
Side chains flipped | 1 |
Waters removed | 107 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 35 |
Residues fitting density worse | 0 |