Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2. |
This entry was created with PDB-REDO version 8.04. |
From original header | |||||||
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Spacegroup | P 63 | a: 150.539 Å | b: 150.539 Å | c: 111.310 Å | α: 90.00° | β: 90.00° | γ: 120.00° |
Resolution | 2.20 Å | Reflections | 71192 | Test set | 3639 (5.1%) | ||
R | 0.1577 | R-free | 0.1777 | ||||
According to PDB-REDO | |||||||
Resolution | 2.20 Å | Reflections | 71192 | Test set | 3639 (5.1%) | Twin | true |
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 | |
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Crystallographic refinement | ||
R | 0.1620 | 0.1430 |
R-free | 0.1800 | 0.1616 |
Bond length RMS Z-score | 0.590 | 0.966 |
Bond angle RMS Z-score | 0.638 | 0.900 |
Model quality | ||
Ramachandran plot normality | -1.818 33 | -1.218 47 |
Rotamer normality | -0.949 78 | -1.893 60 |
Coarse packing | -0.214 51 | -0.244 49 |
Fine packing | -1.693 24 | -1.541 30 |
Bump severity | 0.011 56 | 0.005 74 |
Hydrogen bond satisfaction | 0.899 49 | 0.920 77 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
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Rotamers changed | 7 |
Side chains flipped | 2 |
Waters removed | 16 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 18 |
Residues fitting density worse | 1 |