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Structure of the N-terminal domain (NTD)of SARS-CoV spike protein |
This entry was created with PDB-REDO version 7.32. |
From original header | |||||||
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Spacegroup | P 61 2 2 | a: 73.291 Å | b: 73.291 Å | c: 240.263 Å | α: 90.00° | β: 90.00° | γ: 120.00° |
Resolution | 2.20 Å | Reflections | 20247 | Test set | 1040 (5.1%) | ||
R | 0.2520 | R-free | 0.2820 | ||||
According to PDB-REDO | |||||||
Resolution | 2.20 Å | Reflections | 20247 | Test set | 1040 (5.1%) | ||
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 | 0.2599 | 0.2287 |
R-free | 0.2850 | 0.2734 |
Bond length RMS Z-score | 0.228 | 0.717 |
Bond angle RMS Z-score | 0.556 | 0.890 |
Model quality | ||
Ramachandran plot normality | -3.006 16 | -2.348 24 |
Rotamer normality | -2.288 52 | -2.962 40 |
Coarse packing | -0.619 30 | -0.529 35 |
Fine packing | -1.834 19 | -1.626 26 |
Bump severity | 0.447 2 | 0.711 1 |
Hydrogen bond satisfaction | 0.860 17 | 0.888 36 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 3 |
Side chains flipped | 0 |
Waters removed | 12 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 10 |
Residues fitting density worse | 0 |