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Nanobody H3 AND C1 bound to RBD with Kent mutation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7OAP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.0 M Lithium chloride, 0.1 M Citrate pH 4, 20 % Peg 6000
Crystal Properties Matthews coefficient Solvent content 2.95 58.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.857 α = 90 b = 105.857 β = 90 c = 112.709 γ = 90
Symmetry Space Group P 43 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 2021-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9762 Diamond I04
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 1.55 53 100 0.02 1 16.9 26.8 93033
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 1.55 1.59 93 0.59 0.6 0.6 27.6
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 7oap 1.55 52.984 92354 4722 99.27 0.156 0.155 0.1675 0.1783 0.1915 36.162
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] -1.211 -1.211 2.422
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.114 r_dihedral_angle_4_deg 14.157 r_dihedral_angle_3_deg 12.225 r_rigid_bond_restr 8.608 r_dihedral_angle_1_deg 6.728 r_lrange_other 3.96 r_lrange_it 3.954 r_scangle_it 3.642 r_scangle_other 3.642 r_scbond_it 3.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.114 r_dihedral_angle_4_deg 14.157 r_dihedral_angle_3_deg 12.225 r_rigid_bond_restr 8.608 r_dihedral_angle_1_deg 6.728 r_lrange_other 3.96 r_lrange_it 3.954 r_scangle_it 3.642 r_scangle_other 3.642 r_scbond_it 3.102 r_scbond_other 3.022 r_mcangle_other 2.776 r_mcangle_it 2.774 r_mcbond_it 2.317 r_mcbond_other 2.276 r_angle_refined_deg 1.398 r_angle_other_deg 1.34 r_symmetry_nbd_refined 0.222 r_nbd_refined 0.21 r_symmetry_nbd_other 0.183 r_xyhbond_nbd_refined 0.174 r_nbtor_refined 0.173 r_symmetry_xyhbond_nbd_refined 0.147 r_nbd_other 0.142 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3513 Nucleic Acid Atoms Solvent Atoms 375 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing