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Structure of MERS-Coronavirus Spike Receptor-binding Domain (England1 Strain) in Complex with Vaccine-Elicited Murine Neutralizing Antibody D12 (Crystal Form 1) |
This entry was created with PDB-REDO version 7.32. |
From original header | |||||||
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Spacegroup | P 21 21 21 | a: 74.452 Å | b: 128.790 Å | c: 170.871 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 2.59 Å | Reflections | 51227 | Test set | 2529 (4.9%) | ||
R | 0.2040 | R-free | 0.2440 | ||||
According to PDB-REDO | |||||||
Resolution | 2.59 Å | Reflections | 51227 | Test set | 2529 (4.9%) | Twin | false |
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 | 0.2224 | 0.2075 |
R-free | 0.2509 | 0.2432 |
Bond length RMS Z-score | 0.596 | 0.376 |
Bond angle RMS Z-score | 0.586 | 0.632 |
Model quality | ||
Ramachandran plot normality | -0.121 77 | -0.935 55 |
Rotamer normality | -2.314 52 | -2.304 52 |
Coarse packing | 0.074 66 | 0.143 69 |
Fine packing | 0.318 88 | 0.533 91 |
Bump severity | 0.153 7 | 0.138 8 |
Hydrogen bond satisfaction | 0.880 28 | 0.882 30 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 17 |
Side chains flipped | 0 |
Waters removed | 28 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 2 |
Residues fitting density worse | 0 |