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Crystal Structure of VHH MOD203 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; 32% w/v PEG MME 550
Crystal Properties Matthews coefficient Solvent content 3.18 61.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.49 α = 90 b = 136.49 β = 90 c = 45.284 γ = 120
Symmetry Space Group P 32 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 CMOS RDI CMOS_8M 2024-10-16 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 1.9 44.68 100 0.129 0.999 15.5 10.2 38354
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 1.9 1.94 100 2.743 0.393 1 10.4
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 (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 1.9 44.68 36387 1950 99.98 0.17967 0.178 0.1859 0.21148 0.2183 RANDOM 46.373
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] -0.15 -0.08 -0.15 0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 13 r_dihedral_angle_3_deg 12.931 r_dihedral_angle_1_deg 7.393 r_long_range_B_refined 6.934 r_long_range_B_other 6.934 r_scangle_other 4.864 r_scbond_it 3.285 r_scbond_other 3.284 r_mcangle_it 3.046 r_mcangle_other 3.046
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 13 r_dihedral_angle_3_deg 12.931 r_dihedral_angle_1_deg 7.393 r_long_range_B_refined 6.934 r_long_range_B_other 6.934 r_scangle_other 4.864 r_scbond_it 3.285 r_scbond_other 3.284 r_mcangle_it 3.046 r_mcangle_other 3.046 r_mcbond_it 2.05 r_mcbond_other 2.05 r_angle_refined_deg 1.546 r_angle_other_deg 0.595 r_chiral_restr 0.19 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_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 2484 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms 113
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction