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H6 and F2 nanobodies bound to SARS-CoV-2 spike RBD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7Z1C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.35 47.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.775 α = 90 b = 59.438 β = 90 c = 145.624 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 EIGER2 XE 16M 2021-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.73 59.52 100 0.105 0.031 0.999 11.5 12.5 53452
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.73 1.76 0.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.73 59.438 53238 2623 99.979 0.199 0.1972 0.2057 0.2234 0.2369 38.513
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] 0.963 -0.016 -0.948
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.388 r_dihedral_angle_4_deg 18.145 r_dihedral_angle_3_deg 13.143 r_dihedral_angle_1_deg 7.303 r_lrange_it 5.461 r_lrange_other 5.461 r_scangle_it 2.525 r_scangle_other 2.524 r_scbond_other 1.716 r_scbond_it 1.715
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.388 r_dihedral_angle_4_deg 18.145 r_dihedral_angle_3_deg 13.143 r_dihedral_angle_1_deg 7.303 r_lrange_it 5.461 r_lrange_other 5.461 r_scangle_it 2.525 r_scangle_other 2.524 r_scbond_other 1.716 r_scbond_it 1.715 r_mcangle_it 1.582 r_mcangle_other 1.581 r_angle_refined_deg 1.403 r_angle_other_deg 1.263 r_mcbond_it 1.007 r_mcbond_other 1.006 r_nbd_refined 0.186 r_symmetry_xyhbond_nbd_refined 0.18 r_symmetry_nbd_other 0.177 r_nbtor_refined 0.169 r_nbd_other 0.169 r_xyhbond_nbd_refined 0.153 r_symmetry_nbd_refined 0.128 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.06 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3512 Nucleic Acid Atoms Solvent Atoms 216 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement xia2 data reduction DIALS data scaling PHASER phasing Coot model building