☰ Navigation Tabs
Complex between the Fab arm of AB-3467 and the SARS-CoV-2 receptor binding domain (RBD)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7KZB 7kzb (RBD) and 7czx experimental model PDB 7CZX 7kzb (RBD) and 7czx
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.9 293 Protein complex (5 mg/mL in 25 mM Tris (pH 8.0), 200 mM NaCl) was mixed with an equal volume (2 uL) of well solution comprising 100 mM BisTrisPropane (pH 6.9), 800 mM KSCN, 10% (v/v) glycerol, and 18%(m/v) PEG8000
Crystal Properties Matthews coefficient Solvent content 2.65 53.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.764 α = 90 b = 115.494 β = 90 c = 240.758 γ = 90
Symmetry Space Group C 2 2 21
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 2021-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
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 2.29 48.15 99.8 0.075 0.078 0.021 0.999 22.5 13.7 68595
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 2.29 2.35 97.5 0.747 0.776 0.208 0.882 13.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7kzb (RBD) and 7czx 2.29 48 65175 3368 99.78 0.1966 0.1942 0.2447 0.2336 RANDOM 50.259
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] -0.43 1.63 -1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.401 r_dihedral_angle_4_deg 18.445 r_dihedral_angle_3_deg 15.177 r_dihedral_angle_1_deg 8.188 r_angle_refined_deg 1.722 r_angle_other_deg 1.323 r_chiral_restr 0.076 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.401 r_dihedral_angle_4_deg 18.445 r_dihedral_angle_3_deg 15.177 r_dihedral_angle_1_deg 8.188 r_angle_refined_deg 1.722 r_angle_other_deg 1.323 r_chiral_restr 0.076 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9674 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction