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CRYSTAL STRUCTURE OF SARS-COV-2 RECEPTOR BINDING DOMAIN (RBD-beta variant) in complex with 3D2 Fab and 1D1 Fab
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 COUNTER-DIFFUSION 8.5 293.15 0.1 M Tris pH 8.5
12% PEG 8000
0.2 M AmSO4
Crystal Properties Matthews coefficient Solvent content 2.71 54.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 220.167 α = 90 b = 65.202 β = 94.466 c = 204.023 γ = 90
Symmetry Space Group C 1 2 1
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 EIGER X 16M 2021-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.9763 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.85 50 99.9 0.128 0.138 0.052 0.998 10.8 7 68147
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.85 2.92 100 1.918 2.068 0.769 0.588 7.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.85 49.95 68146 3386 99.916 0.209 0.2063 0.209 0.2617 0.2628 RANDOM 89.655
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] -2.369 -2.42 6.731 -3.936
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.917 r_dihedral_angle_6_deg 12.618 r_lrange_it 11.938 r_lrange_other 11.938 r_mcangle_it 8.931 r_mcangle_other 8.93 r_scangle_it 8.59 r_scangle_other 8.59 r_dihedral_angle_1_deg 7.299 r_dihedral_angle_2_deg 6.042
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.917 r_dihedral_angle_6_deg 12.618 r_lrange_it 11.938 r_lrange_other 11.938 r_mcangle_it 8.931 r_mcangle_other 8.93 r_scangle_it 8.59 r_scangle_other 8.59 r_dihedral_angle_1_deg 7.299 r_dihedral_angle_2_deg 6.042 r_mcbond_it 5.763 r_mcbond_other 5.762 r_scbond_it 5.305 r_scbond_other 5.304 r_angle_refined_deg 1.193 r_angle_other_deg 0.418 r_symmetry_xyhbond_nbd_refined 0.375 r_symmetry_nbd_other 0.196 r_nbd_refined 0.194 r_nbd_other 0.185 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.136 r_symmetry_nbd_refined 0.125 r_ncsr_local_group_2 0.106 r_ncsr_local_group_1 0.1 r_ncsr_local_group_5 0.089 r_symmetry_nbtor_other 0.084 r_ncsr_local_group_4 0.08 r_ncsr_local_group_3 0.062 r_chiral_restr 0.056 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_symmetry_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15942 Nucleic Acid Atoms Solvent Atoms 28 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction