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CRYSTAL STRUCTURE OF SARS-COV-2 RECEPTOR BINDING DOMAIN (RBD-beta variant) in complex with 3D2 Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7LDJ experimental model PDB 5IBT experimental model PDB 3ZL4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 0.04 M potassium dihydrogen phosphate
18 % PEG 8000
20 % glycerol
Crystal Properties Matthews coefficient Solvent content 3.07 59.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.693 α = 90 b = 71.197 β = 90.04 c = 121.245 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 2021-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.9762 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 2.2 48.07 98.9 0.096 0.104 0.039 0.998 13 7.1 44882
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 2.2 2.27 98.3 1.568 1.69 0.627 0.575 7.2
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 (Observed) 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 2.2 48.07 42690 2189 98.69 0.19757 0.19588 0.2014 0.22943 0.2293 RANDOM 53.945
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] 1.44 0.26 0.16 -1.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.049 r_dihedral_angle_4_deg 19.888 r_dihedral_angle_3_deg 15.941 r_long_range_B_other 9.365 r_long_range_B_refined 9.362 r_dihedral_angle_1_deg 8.147 r_scangle_other 7.385 r_mcangle_other 6.713 r_mcangle_it 6.711 r_scbond_it 5.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.049 r_dihedral_angle_4_deg 19.888 r_dihedral_angle_3_deg 15.941 r_long_range_B_other 9.365 r_long_range_B_refined 9.362 r_dihedral_angle_1_deg 8.147 r_scangle_other 7.385 r_mcangle_other 6.713 r_mcangle_it 6.711 r_scbond_it 5.096 r_scbond_other 5.096 r_mcbond_it 4.715 r_mcbond_other 4.709 r_angle_refined_deg 1.614 r_angle_other_deg 1.241 r_chiral_restr 0.064 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4606 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing