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Crystal Structure of VHH MOD239 in complex with SARS-CoV-2 KP.3 RBD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8QH1 experimental model PDB 7KN7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 0.1M Sodium citrate tribasic, pH 5.0; 13% w/v PEG 20,000
Crystal Properties Matthews coefficient Solvent content 3.26 62.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.76 α = 83.61 b = 69.685 β = 82.67 c = 75.43 γ = 89.9
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CMOS RDI CMOS_8M 2024-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.000034 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.1 47.37 91.5 0.144 0.984 7.6 3.6 51184
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 91.1 1.174 0.505 1.1 3.8
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 2.1 39.36 48589 2587 91.46 0.19799 0.19637 0.2021 0.2282 0.23 RANDOM 47.105
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] -2.72 0.27 0.03 0.94 1.07 1.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.969 r_dihedral_angle_1_deg 7.181 r_dihedral_angle_2_deg 6.764 r_long_range_B_refined 6.614 r_long_range_B_other 6.578 r_scangle_other 4.551 r_mcangle_it 2.92 r_mcangle_other 2.92 r_scbond_it 2.844 r_scbond_other 2.844
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.969 r_dihedral_angle_1_deg 7.181 r_dihedral_angle_2_deg 6.764 r_long_range_B_refined 6.614 r_long_range_B_other 6.578 r_scangle_other 4.551 r_mcangle_it 2.92 r_mcangle_other 2.92 r_scbond_it 2.844 r_scbond_other 2.844 r_mcbond_it 1.912 r_mcbond_other 1.912 r_angle_refined_deg 1.297 r_angle_other_deg 0.44 r_chiral_restr 0.057 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 5094 Nucleic Acid Atoms Solvent Atoms 301 Heterogen Atoms 110
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing PDB_EXTRACT data extraction