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The crystal structure of octadecyloxy(naphthalen-1-yl)methylphosphonic acid in complex with red kidney bean purple acid phosphatase |
This entry was created with PDB-REDO version 7.32. |
From original header | |||||||
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Spacegroup | P 31 2 1 | a: 126.174 Å | b: 126.174 Å | c: 298.044 Å | α: 90.00° | β: 90.00° | γ: 120.00° |
Resolution | 2.20 Å | Reflections | 139532 | Test set | 6987 (5.0%) | ||
R | 0.1550 | R-free | 0.1990 | ||||
According to PDB-REDO | |||||||
Resolution | 2.20 Å | Reflections | 139532 | Test set | 6987 (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 | 0.1669 | 0.1717 |
R-free | 0.2060 | 0.2023 |
Bond length RMS Z-score | 0.356 | 0.490 |
Bond angle RMS Z-score | 0.668 | 0.722 |
Model quality | ||
Ramachandran plot normality | -1.237 46 | -0.741 61 |
Rotamer normality | -2.199 54 | -0.904 79 |
Coarse packing | -0.566 33 | -0.547 34 |
Fine packing | -2.412 6 | -2.128 11 |
Bump severity | 0.657 1 | 0.198 5 |
Hydrogen bond satisfaction | 0.881 29 | 0.893 41 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 27 |
Side chains flipped | 1 |
Waters removed | 153 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 3 |
Residues fitting density worse | 1 |