This entry is not up to date with the most recent version of PDB-REDO.
Please log in
to request an update.
Human ectonucleotide pyrophosphatase / phosphodiesterase 3 (ENPP3, NPP3, CD203c) |
This entry was created with PDB-REDO version 7.31. |
From original header | |||||||
---|---|---|---|---|---|---|---|
Spacegroup | P 21 21 21 | a: 96.184 Å | b: 133.640 Å | c: 167.430 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 2.30 Å | Reflections | 87320 | Test set | 1918 (2.2%) | ||
R | 0.1740 | R-free | 0.2140 | ||||
According to PDB-REDO | |||||||
Resolution | 2.30 Å | Reflections | 87320 | Test set | 1918 (2.2%) | ||
Twin | false | Radiation damage | N/A | ||||
PDB-REDO files | |||||||
Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
|||||
Links | |||||||
PDBe | RCSB PDB | 3D bionotes | Proteopedia |
Original | PDB-REDO | |
---|---|---|
Crystallographic refinement | ||
R | 0.1850 | 0.2024 |
R-free | 0.2230 | 0.2439 |
Bond length RMS Z-score | 0.259 | 0.458 |
Bond angle RMS Z-score | 0.595 | 0.716 |
Model quality | ||
Ramachandran plot normality | -1.498 40 | -1.979 30 |
Rotamer normality | -1.203 74 | -2.100 56 |
Coarse packing | -1.287 9 | -1.288 9 |
Fine packing | -2.539 5 | -2.487 5 |
Bump severity | 0.810 0 | 0.063 15 |
Hydrogen bond satisfaction | 0.856 15 | 0.864 19 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 35 |
Side chains flipped | 1 |
Waters removed | 89 |
Peptides flipped | 2 |
Chiralities fixed | 0 |
Residues fitting density better | 2 |
Residues fitting density worse | 19 |