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Crystal Structure of PGT121 Fab Bound to a complex-type sialylated N-glycan |
This entry was created with PDB-REDO version 7.34. |
From PDB header | |||||||
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Spacegroup | P 21 21 21 | a: 67.787 Å | b: 67.787 Å | c: 94.115 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 2.40 Å | Reflections | 20573 | Test set | 1022 (5.0%) | ||
R | 0.2010 | R-free | 0.2490 | ||||
According to PDB-REDO | |||||||
Resolution | 2.21 Å | Reflections | 20573 | Test set | 1022 (5.0%) | Twin | false |
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 |
PDB | PDB-REDO | |
---|---|---|
Crystallographic refinement | ||
R | 0.2678 | 0.2074 |
R-free | 0.2905 | 0.2688 |
Bond length RMS Z-score | 0.278 | 0.565 |
Bond angle RMS Z-score | 0.471 | 0.831 |
Model quality | ||
Ramachandran plot normality | 0.758 60 | 0.326 72 |
Rotamer normality | 0.068 91 | 2.555 47 |
Coarse packing | 0.002 62 | 0.014 61 |
Fine packing | 0.234 78 | 0.171 85 |
Bump severity | 0.306 3 | 0.186 6 |
Hydrogen bond satisfaction | 0.924 81 | 0.931 88 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 3 |
Side chains flipped | 0 |
Waters removed | 13 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 8 |
Residues fitting density worse | 0 |