7Y3N
Crystal structure of SARS-CoV receptor binding domain in complex with human antibody BIOLS56
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.9 | 291 | 20% v/v 2-Propanol, 0.1 M Sodium citrate tribasic dihydrate pH 5.9, 20% w/v Polyethylene glycol 4000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.8 | 67.61 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 112.483 | α = 90 |
b = 159.018 | β = 90 |
c = 175.99 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M | 2021-07-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRF BEAMLINE BL19U1 | 0.97852 | SSRF | BL19U1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||||
1 | 2.97 | 50 | 99.3 | 0.281 | 9.1 | 12.5 | 64593 | 55.17 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.97 | 3.11 | 0.898 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 6LZG, 4TSA | 2.97 | 47.39 | 1.34 | 63804 | 3179 | 97.33 | 0.2226 | 0.2204 | 0.2628 | 52.95 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 17.0023 |
f_angle_d | 0.9319 |
f_chiral_restr | 0.0689 |
f_plane_restr | 0.0063 |
f_bond_d | 0.0053 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 14568 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 52 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHENIX | refinement |
PHASER | phasing |