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The structure of GH101 D764N mutant from Streptococcus pneumoniae TIGR4 in complex with serinyl T-antigen |
This entry was created with PDB-REDO version 7.32. |
From original header | |||||||
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Spacegroup | P 2 21 21 | a: 87.069 Å | b: 121.964 Å | c: 139.605 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 1.80 Å | Reflections | 136577 | Test set | 6863 (5.0%) | ||
R | 0.1490 | R-free | 0.1790 | ||||
According to PDB-REDO | |||||||
Resolution | 1.80 Å | Reflections | 136577 | Test set | 6863 (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 | 0.1435 | 0.1352 |
R-free | 0.1695 | 0.1612 |
Bond length RMS Z-score | 0.559 | 0.395 |
Bond angle RMS Z-score | 0.706 | 0.675 |
Model quality | ||
Ramachandran plot normality | -0.635 64 | -0.435 69 |
Rotamer normality | -0.231 89 | 0.314 95 |
Coarse packing | -0.257 48 | -0.299 46 |
Fine packing | -2.149 11 | -2.079 12 |
Bump severity | 0.002 87 | 0.001 92 |
Hydrogen bond satisfaction | 0.900 50 | 0.906 58 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 24 |
Side chains flipped | 4 |
Waters removed | 147 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 1 |
Residues fitting density worse | 0 |