☰ Navigation Tabs
An ultra-potent human neutralizing antibody locks the SARS-CoV-2 spike in the closed conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other homology model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Magnesium chloride hexahydrate, 0.1 M TRIS pH 8.5, 30% (w/v) PEG 4000
Condition A1 of Molecular Dimensions SG1 HT-96 Eco Screen
Crystal Properties Matthews coefficient Solvent content 2.26 45.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.014 α = 90 b = 85.722 β = 90 c = 86.306 γ = 90
Symmetry Space Group P 21 21 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 2020-09-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0 SLS X10SA
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 1.38 48.15 99.3 0.059 0.064 0.024 0.999 19.1 13.1 89367
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 1.38 1.4 87.8 2.115 2.295 0.881 0.74 1.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT homology model 1.38 40 84581 4458 99.72 0.2002 0.1993 0.2068 0.215 0.2061 RANDOM 27.198
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] -0.73 1.63 -0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.257 r_dihedral_angle_4_deg 18.295 r_dihedral_angle_3_deg 12.351 r_dihedral_angle_1_deg 7.375 r_angle_other_deg 1.237 r_angle_refined_deg 1.226 r_chiral_restr 0.046 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.257 r_dihedral_angle_4_deg 18.295 r_dihedral_angle_3_deg 12.351 r_dihedral_angle_1_deg 7.375 r_angle_other_deg 1.237 r_angle_refined_deg 1.226 r_chiral_restr 0.046 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3339 Nucleic Acid Atoms Solvent Atoms 326 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction XDS data reduction