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Crystal structure of the human astrovirus serotype 8 capsid spike in complex with scFv 2D9, an astrovirus-neutralizing antibody, at 2.65-A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QSQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 295.15 0.1 M ammonium acetate, 0.1 M Bis-Tris pH 5.5, 16 % PEG 10,000
Crystal Properties Matthews coefficient Solvent content 2.41 48.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.592 α = 90 b = 97.34 β = 90 c = 208.307 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 100 PIXEL DECTRIS PILATUS3 S 6M 2018-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.115830 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.65 208.31 100 0.451 0.454 0.051 0.998 16 76.5 30304 42.48
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.78 99.8 3.877 3.907 0.471 0.692 66.6
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 THROUGHOUT 3QSQ 2.65 104.15 1.33 30211 1998 99.87 0.2201 0.2182 0.2185 0.2469 0.2464 40.0268
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6922 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing PDB_EXTRACT data extraction