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B5-5 nanobody bound to SARS-CoV-2 spike RBD (Wuhan)
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 Tris pH 8.5, PEG smear low
Seeded from crystals grown in ammonium nitrate, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.37 48.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.038 α = 90 b = 70.029 β = 90 c = 109.005 γ = 90
Symmetry Space Group P 2 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 2022-12-12 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) 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 1.969 45.079 99.9 0.2 0.203 0.038 0.999 15.3 53.6 25155
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 1.97 2.02 7.33 7.458 1.373 0.461 55.5
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 1.969 45.079 25113 1264 99.861 0.183 0.1806 0.1805 0.2231 0.2231 51.534
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] 1.966 -1.465 -0.501
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.409 r_dihedral_angle_3_deg 15.112 r_lrange_it 9.923 r_lrange_other 9.921 r_dihedral_angle_2_deg 9.156 r_dihedral_angle_1_deg 7.695 r_scangle_it 7.684 r_scangle_other 7.682 r_mcangle_it 5.823 r_mcangle_other 5.822
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.409 r_dihedral_angle_3_deg 15.112 r_lrange_it 9.923 r_lrange_other 9.921 r_dihedral_angle_2_deg 9.156 r_dihedral_angle_1_deg 7.695 r_scangle_it 7.684 r_scangle_other 7.682 r_mcangle_it 5.823 r_mcangle_other 5.822 r_scbond_it 5.513 r_scbond_other 5.511 r_mcbond_it 4.283 r_mcbond_other 4.282 r_angle_refined_deg 2.182 r_angle_other_deg 0.684 r_symmetry_xyhbond_nbd_refined 0.463 r_symmetry_nbd_refined 0.29 r_xyhbond_nbd_refined 0.223 r_nbd_refined 0.221 r_symmetry_nbd_other 0.21 r_nbd_other 0.204 r_nbtor_refined 0.197 r_symmetry_xyhbond_nbd_other 0.17 r_chiral_restr 0.095 r_symmetry_nbtor_other 0.095 r_bond_refined_d 0.016 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2496 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement xia2.multiplex data reduction Aimless data scaling PHASER phasing Coot model building PARROT phasing