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Crystal structure of H5 hemagglutinin mutant Y161A from A/Viet Nam/1203/2004 H5N1 influenza virus in complex with 3'-GcLN |
This entry was created with PDB-REDO version 8.03. |
From original header | |||||||
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Spacegroup | P 1 21 1 | a: 66.555 Å | b: 231.070 Å | c: 71.295 Å | α: 90.00° | β: 97.04° | γ: 90.00° |
Resolution | 3.30 Å | Reflections | 31127 | Test set | 1656 (5.3%) | ||
R | 0.2394 | R-free | 0.2803 | ||||
According to PDB-REDO | |||||||
Resolution | 3.30 Å | Reflections | 31127 | Test set | 1656 (5.3%) | ||
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 | 0.2563 | 0.2164 |
R-free | 0.3012 | 0.2412 |
Bond length RMS Z-score | 0.470 | 0.328 |
Bond angle RMS Z-score | 0.631 | 0.565 |
Model quality | ||
Ramachandran plot normality | -4.252 8 | -4.475 7 |
Rotamer normality | -3.113 38 | -3.416 33 |
Coarse packing | -1.153 12 | -0.494 36 |
Fine packing | -2.037 13 | -1.285 41 |
Bump severity | 0.273 4 | 0.103 10 |
Hydrogen bond satisfaction | 0.770 3 | 0.809 6 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 15 |
Side chains flipped | 0 |
Waters removed | 0 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 67 |
Residues fitting density worse | 0 |