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H11-D4, SARS-CoV-2 RBD, CR3022 ternary complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YZ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 Purified RBD, Fab CR3022 and nanobody H11-D4 were mixed together at a molar ratio of 1:1:1 to a final concentration of approximately 7 mg/ml and incubated at room temperature for one hour. Initial screening was performed in 96-well plates using the nanolitre sitting-drop vapour diffusion method. The best crystals were grown in condition containing 0.1 M sodium citrate tribasic dihydrate, pH 5.0, 10% (w/v) Polyethylene glycol 6000.
Crystal Properties Matthews coefficient Solvent content 4.05 69.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.717 α = 90 b = 150.395 β = 90 c = 119.537 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2020-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall 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 2.71 106.1 99 0.231 0.065 0.997 7.4 13.2 73071
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.71 2.76 94 3.953 0.087 0.2 9
Refinement Statistics 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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6YZ7 2.71 74.86 1.35 47412 2365 64.33 0.2004 0.1983 0.199 0.241 0.2405 53.5819
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11699 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 28
Software Software Software Name Purpose XDS data reduction PHASER phasing PHENIX refinement PDB_EXTRACT data extraction XSCALE data scaling