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Crystal structure of 1918 pandemic influenza virus hemagglutinin mutant D225G complexed with avian receptor analogue LSTa |
This entry was created with PDB-REDO version 8.04. |
From original header | |||||||
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Spacegroup | P 1 21 1 | a: 71.986 Å | b: 243.195 Å | c: 72.208 Å | α: 90.00° | β: 119.62° | γ: 90.00° |
Resolution | 2.81 Å | Reflections | 52303 | Test set | 2670 (5.1%) | ||
R | 0.2014 | R-free | 0.2460 | ||||
According to PDB-REDO | |||||||
Resolution | 2.80 Å | Reflections | 52303 | Test set | 2670 (5.1%) | ||
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 | 0.2100 | 0.1919 |
R-free | 0.2515 | 0.2253 |
Bond length RMS Z-score | 0.525 | 0.481 |
Bond angle RMS Z-score | 0.745 | 0.660 |
Model quality | ||
Ramachandran plot normality | -3.931 10 | -2.133 27 |
Rotamer normality | -2.867 42 | -2.277 53 |
Coarse packing | -0.364 43 | -0.120 55 |
Fine packing | -1.697 24 | -1.361 38 |
Bump severity | 0.221 5 | 0.071 14 |
Hydrogen bond satisfaction | 0.876 25 | 0.877 26 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 46 |
Side chains flipped | 0 |
Waters removed | 31 |
Peptides flipped | 5 |
Chiralities fixed | 0 |
Residues fitting density better | 12 |
Residues fitting density worse | 0 |