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Nanobody C5 bound to Kent variant RBD (N501Y)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7OAO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Ammonium fluoride and 20 % Peg 3350
Crystal Properties Matthews coefficient Solvent content 2.19 43.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 28.81 α = 90 b = 153.73 β = 100.33 c = 75.85 γ = 90
Symmetry Space Group P 1 21 1
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 2021-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9999 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.65 39 100 0.044 1 10 6.6 77705
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.69 100 0.56 0.6 1.2 6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7OAO 1.65 38.462 77679 3776 99.967 0.177 0.1754 0.1848 0.1992 0.2088 29.12
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] 0.02 0.707 -2.163 1.768
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.749 r_dihedral_angle_4_deg 16.287 r_dihedral_angle_3_deg 11.56 r_dihedral_angle_1_deg 6.913 r_lrange_it 5.963 r_lrange_other 5.961 r_scangle_it 3.356 r_scangle_other 3.355 r_scbond_it 2.179 r_scbond_other 2.179
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.749 r_dihedral_angle_4_deg 16.287 r_dihedral_angle_3_deg 11.56 r_dihedral_angle_1_deg 6.913 r_lrange_it 5.963 r_lrange_other 5.961 r_scangle_it 3.356 r_scangle_other 3.355 r_scbond_it 2.179 r_scbond_other 2.179 r_mcangle_it 1.893 r_mcangle_other 1.892 r_angle_refined_deg 1.337 r_angle_other_deg 1.323 r_mcbond_it 1.314 r_mcbond_other 1.314 r_nbd_refined 0.18 r_symmetry_nbd_other 0.173 r_nbtor_refined 0.168 r_symmetry_nbd_refined 0.159 r_nbd_other 0.159 r_xyhbond_nbd_refined 0.152 r_symmetry_xyhbond_nbd_refined 0.136 r_symmetry_nbtor_other 0.073 r_ncsr_local_group_2 0.064 r_chiral_restr 0.06 r_ncsr_local_group_1 0.056 r_bond_refined_d 0.007 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 4892 Nucleic Acid Atoms Solvent Atoms 470 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing