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Crystal structure of the HCoV-HKU1 RBD in complex with Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model SwissModel experimental model PDB 5KWB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 293 0.2% (w/v) Ala-Ala, 0.2% (w/v) Ala-Gln, 0.2% (w/v) Gly-Glu, 0.2% (w/v) Gly-L-Ala, 0.2% (w/v) Gly-L-Asp, 0.2% (w/v) Gly-Sar, 0.2% (w/v) L-Carnosine, 0.2% (w/v) Leu-Ala hydrate, 0.1 M Buffer System 3 [Tris (base); BICINE] pH 8.5, 20% (v/v) PEG 500* MME, 10 % w/v PEG 20,000; for TMPRSS2:VHH77, 0.2 M sodium malonate pH 6.0, 10% (w/v) Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.65 53.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.235 α = 90 b = 161.286 β = 108.94 c = 57.06 γ = 90
Symmetry Space Group P 1 21 1
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 S 9M 2024-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97918 SSRF BL02U1
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 1.8 30.74 99.7 0.093 0.101 0.997 11.65 6.5 79102
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.91 0.601 0.651 0.877
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.8 30.74 1.39 79025 3955 99.81 0.1744 0.1729 0.172 0.2029 0.2019
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 13.044 f_angle_d 0.86 f_chiral_restr 0.056 f_plane_restr 0.007 f_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5512 Nucleic Acid Atoms Solvent Atoms 640 Heterogen Atoms 52
Software Software Software Name Purpose PHENIX refinement XDS data scaling XDS data reduction PHASER phasing