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Crystal structure of human NA-63 Fab in complex with neuraminidase from A/Hunan/02650/2016(H7N9) |
This entry was created with PDB-REDO version 8.04. |
From original header | |||||||
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Spacegroup | P 4 21 2 | a: 164.576 Å | b: 164.576 Å | c: 192.575 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 2.80 Å | Reflections | 63498 | Test set | 3291 (5.2%) | ||
R | 0.2031 | R-free | 0.2486 | ||||
According to PDB-REDO | |||||||
Resolution | 2.80 Å | Reflections | 63498 | Test set | 3291 (5.2%) | ||
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 | 0.2172 | 0.2131 |
R-free | 0.2551 | 0.2426 |
Bond length RMS Z-score | 0.677 | 0.307 |
Bond angle RMS Z-score | 0.807 | 0.553 |
Model quality | ||
Ramachandran plot normality | -1.956 30 | -2.497 22 |
Rotamer normality | -5.744 10 | -3.373 34 |
Coarse packing | -0.723 26 | -0.490 37 |
Fine packing | -1.571 29 | -0.997 53 |
Bump severity | 0.237 4 | 0.123 9 |
Hydrogen bond satisfaction | 0.828 8 | 0.836 10 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 33 |
Side chains flipped | 0 |
Waters removed | 5 |
Peptides flipped | 24 |
Chiralities fixed | 0 |
Residues fitting density better | 13 |
Residues fitting density worse | 2 |