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Crystal structure of SARS-CoV-1 RBD in complex with nanobody aSR29 and aSR347
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7LM9 experimental model PDB 8CWV chain_b experimental model PDB 7KN5 chain_e
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 20% w/v PEG4000, 0.1 M Tris 8.0
Crystal Properties Matthews coefficient Solvent content 3.51 64.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.852 α = 90 b = 134.679 β = 90 c = 136.688 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 103.15 PIXEL DECTRIS EIGER X 16M 2022-08-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.979021 SSRF BL10U2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.599 95.93 99.1 0.121 0.129 0.998 15.1 7.7 83452 52.57
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.74 99.7 1.191 0.784 7.97
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.599 47.967 1.34 83452 4176 98.82 0.2346 0.2323 0.2335 0.2793 0.2801 Random selection
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 8.089 f_angle_d 0.634 f_chiral_restr 0.076 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6983 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 30
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling autoPROC data reduction PHENIX phasing