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Soaking competent crystal form of the SARS-CoV-2 Receptor Binding Domain (RBD):CR3022 complex.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6W41
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.7 293 0.1 M SODIUM MALONATE, 0.1 M TRIS PH 7.7, 22% W/V POLYETHYLENE GLYCOL 1,000
Crystal Properties Matthews coefficient Solvent content 5.13 76.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 207.13 α = 90 b = 207.13 β = 90 c = 199.866 γ = 90
Symmetry Space Group P 41 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 PILATUS3 6M 2020-05-20 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) 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 3.09 68.028 91.1 0.933 4.6 4.7 72060
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 3.09 3.16 90.6 0.415 1.5 4.6
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 6W41 3.1 68.028 71615 3669 90.525 0.219 0.2176 0.217 0.2472 0.2474 55.64
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] 0.063 0.063 -0.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.099 r_dihedral_angle_3_deg 16.873 r_dihedral_angle_4_deg 16.11 r_lrange_it 13.544 r_lrange_other 13.544 r_scangle_it 8.243 r_scangle_other 8.243 r_mcangle_it 8.047 r_mcangle_other 8.047 r_dihedral_angle_1_deg 7.622
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.099 r_dihedral_angle_3_deg 16.873 r_dihedral_angle_4_deg 16.11 r_lrange_it 13.544 r_lrange_other 13.544 r_scangle_it 8.243 r_scangle_other 8.243 r_mcangle_it 8.047 r_mcangle_other 8.047 r_dihedral_angle_1_deg 7.622 r_scbond_it 5.153 r_scbond_other 5.149 r_mcbond_it 4.992 r_mcbond_other 4.992 r_angle_refined_deg 1.548 r_angle_other_deg 1.227 r_symmetry_nbd_refined 0.21 r_nbd_other 0.192 r_symmetry_nbd_other 0.189 r_symmetry_xyhbond_nbd_refined 0.187 r_xyhbond_nbd_refined 0.185 r_nbd_refined 0.183 r_nbtor_refined 0.169 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.057 r_ncsr_local_group_9 0.039 r_ncsr_local_group_5 0.031 r_ncsr_local_group_8 0.03 r_ncsr_local_group_4 0.029 r_ncsr_local_group_6 0.027 r_ncsr_local_group_1 0.025 r_ncsr_local_group_7 0.024 r_ncsr_local_group_2 0.023 r_ncsr_local_group_3 0.023 r_bond_refined_d 0.008 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 14694 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing