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Crystal structure of the Wuhan SARS-CoV-2 Spike RBD (319-541) complexed with 1p1B10 nanobody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M MES monohydrate pH 6.0, 20% w/v Polyethylene glycol monomethyl ether 2,000
Crystal Properties Matthews coefficient Solvent content 2.04 39.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.33 α = 90 b = 47.05 β = 102.991 c = 60.15 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 EIGER2 S 16M 2024-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17UM 0.979183 SSRF BL17UM
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 1.55 48.38 98.6 0.064 0.088 0.06 0.998 10.1 3.4 49833
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) 1.55 1.58 98.8 1.119 1.509 1.005 0.431 1 3.4
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.55 48.376 49831 2403 98.486 0.176 0.1739 0.1739 0.2083 0.2084 27.02
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] -0.109 0.482 0.106 -0.199
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.692 r_dihedral_angle_2_deg 14.402 r_dihedral_angle_3_deg 11.691 r_dihedral_angle_1_deg 7.959 r_lrange_it 6.329 r_lrange_other 6.217 r_scangle_it 3.914 r_scangle_other 3.913 r_mcangle_it 2.662 r_mcangle_other 2.662
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.692 r_dihedral_angle_2_deg 14.402 r_dihedral_angle_3_deg 11.691 r_dihedral_angle_1_deg 7.959 r_lrange_it 6.329 r_lrange_other 6.217 r_scangle_it 3.914 r_scangle_other 3.913 r_mcangle_it 2.662 r_mcangle_other 2.662 r_scbond_it 2.597 r_scbond_other 2.574 r_angle_refined_deg 2.138 r_mcbond_it 1.741 r_mcbond_other 1.732 r_angle_other_deg 0.844 r_nbd_refined 0.195 r_nbtor_refined 0.175 r_symmetry_nbd_other 0.166 r_symmetry_nbd_refined 0.143 r_xyhbond_nbd_refined 0.14 r_nbd_other 0.129 r_symmetry_xyhbond_nbd_refined 0.125 r_chiral_restr 0.114 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.013 r_gen_planes_refined 0.013 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2505 Nucleic Acid Atoms Solvent Atoms 364 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing