☰ Navigation Tabs
Crystallographic structure of two neutralizing nanobodies in complex with SARS-CoV-2 spike receptor-binding Domain (RBD)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NC2 4NC2, 5IMK, 6M0J experimental model PDB 5IMK 4NC2, 5IMK, 6M0J experimental model PDB 6M0J 4NC2, 5IMK, 6M0J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 0.1 M (NH4)2SO4 0.1 M TRIS pH7.5 20% (w/v) PEG1500
Crystal Properties Matthews coefficient Solvent content 3.99 69.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.456 α = 90 b = 154.456 β = 90 c = 257.916 γ = 120
Symmetry Space Group P 65 2 2
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 X 9M 2021-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.979 SSRF BL17U1
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 3.2 49.54 100 0.153 0.157 0.036 0.999 20.3 18.5 30769
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 3.2 3.37 100 1.261 1.296 0.296 0.865 19
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 4NC2, 5IMK, 6M0J 3.2 49.5 29121 1554 99.85 0.2102 0.2075 0.2119 0.2628 0.2664 RANDOM 91.737
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] 0.83 0.41 0.83 -2.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.936 r_dihedral_angle_4_deg 16.891 r_dihedral_angle_3_deg 16.857 r_dihedral_angle_1_deg 6.137 r_angle_other_deg 2.435 r_angle_refined_deg 1.702 r_chiral_restr 0.168 r_bond_other_d 0.036 r_bond_refined_d 0.013 r_gen_planes_other 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.936 r_dihedral_angle_4_deg 16.891 r_dihedral_angle_3_deg 16.857 r_dihedral_angle_1_deg 6.137 r_angle_other_deg 2.435 r_angle_refined_deg 1.702 r_chiral_restr 0.168 r_bond_other_d 0.036 r_bond_refined_d 0.013 r_gen_planes_other 0.01 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6937 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction