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RBD domain of SARS-CoV2 in complex with neutralizing nanobody NM1226
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Z1Z 6Z1Z, 6XC4 experimental model PDB 6XC4 6Z1Z, 6XC4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 277 50mM K2HPO4, 20% (w/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 3.8 67.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.093 α = 90 b = 128.093 β = 90 c = 77.676 γ = 90
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 2M 2020-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.9999 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.297 46.103 99.9 0.999 19.5 9.1 28115
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 2.297 2.44 99.6 0.484 1.4
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 6Z1Z, 6XC4 2.3 46.103 28115 1687 99.908 0.187 0.1843 0.1894 0.2239 0.2299 59.942
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] 0.682 0.682 -1.364
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.612 r_dihedral_angle_4_deg 19.526 r_dihedral_angle_3_deg 15.138 r_lrange_other 8.578 r_lrange_it 8.57 r_dihedral_angle_1_deg 7.715 r_scangle_it 5.482 r_scangle_other 5.426 r_mcangle_other 5.264 r_mcangle_it 5.262
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.612 r_dihedral_angle_4_deg 19.526 r_dihedral_angle_3_deg 15.138 r_lrange_other 8.578 r_lrange_it 8.57 r_dihedral_angle_1_deg 7.715 r_scangle_it 5.482 r_scangle_other 5.426 r_mcangle_other 5.264 r_mcangle_it 5.262 r_scbond_it 3.99 r_scbond_other 3.87 r_mcbond_it 3.653 r_mcbond_other 3.64 r_angle_refined_deg 1.463 r_angle_other_deg 1.262 r_symmetry_nbd_refined 0.223 r_nbd_other 0.207 r_nbd_refined 0.19 r_symmetry_nbd_other 0.179 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.142 r_symmetry_xyhbond_nbd_refined 0.142 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.066 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 2503 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing