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Crystal Structure of ADP ribose phosphatase of NSP3 from SARS CoV-2 |
This entry was created with PDB-REDO version 8.04. |
From original header | |||||||
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Spacegroup | P 1 | a: 30.391 Å | b: 37.896 Å | c: 65.400 Å | α: 84.37° | β: 82.11° | γ: 90.11° |
Resolution | 2.03 Å | Reflections | 15783 | Test set | 770 (4.9%) | ||
R | 0.1864 | R-free | 0.2335 | ||||
According to PDB-REDO | |||||||
Resolution | 2.03 Å | Reflections | 15783 | Test set | 770 (4.9%) | ||
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 | 0.1996 | 0.1697 |
R-free | 0.2350 | 0.2280 |
Bond length RMS Z-score | 0.463 | 0.254 |
Bond angle RMS Z-score | 0.663 | 0.476 |
Model quality | ||
Ramachandran plot normality | -0.789 59 | -0.367 71 |
Rotamer normality | -1.562 67 | -0.588 84 |
Coarse packing | 1.464 98 | 1.593 98 |
Fine packing | -1.220 44 | -0.989 53 |
Bump severity | 0.004 78 | 0.005 74 |
Hydrogen bond satisfaction | 0.915 71 | 0.917 73 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 9 |
Side chains flipped | 0 |
Waters removed | 12 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 7 |
Residues fitting density worse | 0 |