☰ Navigation Tabs
SARS-CoV-2 spike RBD with A8 and H3 nanobodies bound
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 NaCl, potassium citrate pH 4.2, PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.43 49.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.609 α = 90 b = 97.197 β = 90 c = 117.583 γ = 90
Symmetry Space Group P 21 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 2021-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 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 2.14 58.78 100 0.088 0.996 6.5 13.7 57917
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 2.14 2.18 0.324
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 2.37 58.78 42863 2056 99.991 0.214 0.2126 0.2183 0.249 0.2545 54.72
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] -0.246 0.218 0.027
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.027 r_dihedral_angle_4_deg 14.816 r_dihedral_angle_3_deg 13.613 r_dihedral_angle_1_deg 6.771 r_lrange_it 3.921 r_lrange_other 3.913 r_scangle_it 2.249 r_scangle_other 2.249 r_mcangle_it 1.85 r_mcangle_other 1.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.027 r_dihedral_angle_4_deg 14.816 r_dihedral_angle_3_deg 13.613 r_dihedral_angle_1_deg 6.771 r_lrange_it 3.921 r_lrange_other 3.913 r_scangle_it 2.249 r_scangle_other 2.249 r_mcangle_it 1.85 r_mcangle_other 1.85 r_scbond_it 1.382 r_scbond_other 1.335 r_angle_refined_deg 1.241 r_mcbond_it 1.142 r_mcbond_other 1.142 r_angle_other_deg 1.119 r_nbd_other 0.188 r_nbd_refined 0.174 r_nbtor_refined 0.166 r_symmetry_nbd_other 0.164 r_symmetry_nbd_refined 0.139 r_symmetry_xyhbond_nbd_refined 0.127 r_xyhbond_nbd_refined 0.121 r_ncsr_local_group_1 0.088 r_ncsr_local_group_2 0.073 r_ncsr_local_group_3 0.071 r_symmetry_nbtor_other 0.068 r_chiral_restr 0.042 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6960 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement xia2 data reduction DIALS data scaling PHASER phasing Coot model building