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The crystal structure of Nsp9 RNA binding protein of SARS CoV-2 |
This entry was created with PDB-REDO version 8.04 using the deposited PDB model version 1.3 |
From original header | |||||||
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Spacegroup | P 61 2 2 | a: 89.883 Å | b: 89.883 Å | c: 132.587 Å | α: 90.00° | β: 90.00° | γ: 120.00° |
Resolution | 2.95 Å | Reflections | 6937 | Test set | 0 (0.0%) | ||
R | 0.2398 | R-free | 0.2760 | ||||
According to PDB-REDO | |||||||
Resolution | 2.95 Å | Reflections | 6937 | Test set | 709 (10.2%) New test set, PDB-REDO compensated for this | ||
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 | |
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Crystallographic refinement | ||
R | 0.2702 | 0.2259 |
R-free | 0.3270 R-free was considered biased, the estimated unbiased R-free was used | 0.3034 |
Bond length RMS Z-score | 0.445 | 0.451 |
Bond angle RMS Z-score | 0.608 | 0.748 |
Model quality | ||
Ramachandran plot normality | -2.331 24 | -3.176 15 |
Rotamer normality | -4.527 20 | -6.135 8 |
Coarse packing | -0.665 28 | -0.894 19 |
Fine packing | -1.225 43 | -1.109 48 |
Bump severity | 0.044 21 | 0.161 7 |
Hydrogen bond satisfaction | 0.886 34 | 0.869 21 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 3 |
Side chains flipped | 11 |
Waters removed | 0 |
Peptides flipped | 6 |
Chiralities fixed | 0 |
Residues fitting density better | 19 |
Residues fitting density worse | 4 |