6YLA
Crystal structure of the SARS-CoV-2 receptor binding domain in complex with CR3022 Fab
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 0.1 M Sodium malonate, 0.1 M Tris pH 8.0 and 30% w/v Polyethylene glycol 1,000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.28 | 71.23 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 163.124 | α = 90 |
b = 163.124 | β = 90 |
c = 189.076 | γ = 90 |
Symmetry | |
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Space Group | P 41 21 2 |
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 EIGER2 XE 16M | 2020-04-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.9762 | Diamond | I03 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | 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 | 2.42 | 58.8 | 100 | 0.303 | 0.034 | 0.997 | 11.6 | 78.7 | 97407 | 72.83 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.42 | 2.46 | 0.45 |
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 | 6M0J, 4KMT, 5I1D, 6YM0 | 2.42 | 55.31 | 1.33 | 94154 | 4837 | 96.77 | 0.2139 | 0.2127 | 0.2367 | 89.23 |
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 | 17.7654 |
f_angle_d | 0.5215 |
f_chiral_restr | 0.0463 |
f_plane_restr | 0.0043 |
f_bond_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9947 |
Nucleic Acid Atoms | |
Solvent Atoms | 52 |
Heterogen Atoms | 87 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
PHENIX | refinement |
xia2 | data reduction |
xia2 | data scaling |
PHASER | phasing |