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Crystal structure of a GII.4 norovirus capsid P domain in complex with neutralizing antibody 24C10
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model SwissModel experimental model PDB 5KON
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 297.15 0.2 M HEPES: NaOH, pH 7.5, 8 % (w/v) PEG 8000, 8 % (v/v) Ethylene Glycol
Crystal Properties Matthews coefficient Solvent content 2.7 54.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.117 α = 90 b = 56.428 β = 99.574 c = 182.117 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 PILATUS 6M 2024-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.7 47.78 99.8 0.1463 0.998 12.22 13.6 49114 53.6
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 2.7 2.77 0.723
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 2.7 47.78 1.36 49107 1992 99.8 0.2099 0.2084 0.2084 0.2455 0.2449 59.52
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 13.7167 f_angle_d 0.6837 f_chiral_restr 0.0477 f_plane_restr 0.0055 f_bond_d 0.0037
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11181 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement DIALS data reduction DIALS data scaling PHENIX phasing