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Crystal structure of the SARS-CoV-2 RBD in complex with a human single domain antibody n3113
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LZG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 4.3M sodium chloride and 0.1M HEPES, pH 7.5
Crystal Properties Matthews coefficient Solvent content 5.05 75.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.21 α = 90 b = 146.21 β = 90 c = 93.08 γ = 120
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 2020-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.979 SSRF BL17U1
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 2.27 73.11 99.9 0.997 11.1 10.4 34264 37.75
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 2.27 2.33 0.798
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6LZG 2.27 42.56 1.97 34237 1974 99.81 0.1783 0.1767 0.1852 0.2033 0.2017 40.35
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 3.684 f_angle_d 0.9544 f_chiral_restr 0.0559 f_bond_d 0.0076 f_plane_restr 0.0054
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2600 Nucleic Acid Atoms Solvent Atoms 245 Heterogen Atoms 14
Software Software Software Name Purpose autoPROC data processing PHENIX refinement PHASER phasing Coot model building XDS data reduction XDS data scaling