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Nanobody H11 and F2 bound to RBD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ZBP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M BICINE pH 8.5, 20% w/v Polyethylene glycol 10,000
Crystal Properties Matthews coefficient Solvent content 3.99 69.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.01 α = 90 b = 191.59 β = 90 c = 56.87 γ = 90
Symmetry Space Group P 21 21 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 PILATUS 6M 2020-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 2.59 59.16 100 0.125 0.999 14.6 13.6 54473
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 2.59 2.66 0.331
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 6ZBP 2.59 59.16 51758 2632 99.93 0.20991 0.20832 0.2138 0.24067 0.241 RANDOM 101
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] 6.34 -0.43 -5.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.979 r_dihedral_angle_3_deg 17.194 r_dihedral_angle_4_deg 16.954 r_dihedral_angle_1_deg 7.943 r_long_range_B_refined 6.946 r_long_range_B_other 6.946 r_scangle_other 5.11 r_mcangle_it 4.451 r_mcangle_other 4.451 r_scbond_it 3.214
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.979 r_dihedral_angle_3_deg 17.194 r_dihedral_angle_4_deg 16.954 r_dihedral_angle_1_deg 7.943 r_long_range_B_refined 6.946 r_long_range_B_other 6.946 r_scangle_other 5.11 r_mcangle_it 4.451 r_mcangle_other 4.451 r_scbond_it 3.214 r_scbond_other 3.214 r_mcbond_it 2.865 r_mcbond_other 2.865 r_angle_refined_deg 1.613 r_angle_other_deg 1.247 r_chiral_restr 0.063 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 7070 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing