Complex structure of MERS-CoV spike RBD bound to CD26 |
This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 2.2 |
From original header | |||||||
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Spacegroup | P 61 2 2 | a: 110.224 Å | b: 110.224 Å | c: 527.599 Å | α: 90.00° | β: 90.00° | γ: 120.00° |
Resolution | 2.70 Å | Reflections | 53442 | Test set | 2712 (5.1%) | ||
R | 0.1982 | R-free | 0.2324 | ||||
According to PDB-REDO | |||||||
Resolution | 2.70 Å | Reflections | 53442 | Test set | 2712 (5.1%) | ||
Twin | false | Radiation damage | 26 | ||||
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 | 0.2135 | 0.1869 |
R-free | 0.2403 | 0.2266 |
Bond length RMS Z-score | 0.592 | 0.392 |
Bond angle RMS Z-score | 0.746 | 0.615 |
Model quality | ||
Ramachandran plot normality | -2.357 25 | -2.133 29 |
Rotamer normality | -3.026 32 | -2.204 47 |
Coarse packing | 0.181 57 | 0.152 56 |
Fine packing | -1.356 38 | -1.347 38 |
Bump severity | 0.532 1 | 0.472 2 |
Hydrogen bond satisfaction | 0.849 13 | 0.853 15 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 16 |
Side chains flipped | 0 |
Waters removed | 28 |
Peptides flipped | 2 |
Chiralities fixed | 0 |
Residues fitting density better | 19 |
Residues fitting density worse | 0 |