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RBD domain SARS-CoV2 in complex with neutralizing nanobody NM1230
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6XC4 6XC4, 6Z1Z experimental model PDB 6Z1Z 6XC4, 6Z1Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.9 293 200 mM MgCl2, 20% (w/v) PEG 3350, pH 5.9
Crystal Properties Matthews coefficient Solvent content 2.55 51.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.29 α = 90 b = 63.29 β = 90 c = 411.91 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 90 PIXEL DECTRIS EIGER X 16M 2020-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.999998 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.9 46.5 93.5 0.207 0.998 7.8 6.06 18493 61
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 2.98 95.7 1.86 0.662 1.15
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 6XC4, 6Z1Z 2.902 30.002 18475 1293 93.44 0.269 0.2661 0.2659 0.3051 0.305 67.189
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] 4.256 4.256 -8.511
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.602 r_dihedral_angle_3_deg 19.805 r_dihedral_angle_4_deg 17.164 r_lrange_it 6.835 r_lrange_other 6.832 r_mcangle_it 4.561 r_mcangle_other 4.56 r_dihedral_angle_1_deg 4.015 r_scangle_it 3.86 r_scangle_other 3.859
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.602 r_dihedral_angle_3_deg 19.805 r_dihedral_angle_4_deg 17.164 r_lrange_it 6.835 r_lrange_other 6.832 r_mcangle_it 4.561 r_mcangle_other 4.56 r_dihedral_angle_1_deg 4.015 r_scangle_it 3.86 r_scangle_other 3.859 r_mcbond_it 2.695 r_mcbond_other 2.691 r_scbond_it 2.232 r_scbond_other 2.231 r_angle_refined_deg 1.217 r_angle_other_deg 1.047 r_symmetry_xyhbond_nbd_other 0.286 r_symmetry_nbd_refined 0.236 r_xyhbond_nbd_refined 0.205 r_symmetry_nbd_other 0.173 r_nbtor_refined 0.164 r_nbd_refined 0.162 r_nbd_other 0.159 r_symmetry_nbtor_other 0.071 r_symmetry_xyhbond_nbd_refined 0.054 r_chiral_restr 0.031 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4831 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing