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Structural basis for broad detection of genogroup II noroviruses by a monoclonal antibody that binds to a site occluded in the viral particle
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ONU 3ONU for P domain, i.e., chains A and B and 1WEJ for Fab, i.e., chains D,E, F, G experimental model PDB 1WEJ 3ONU for P domain, i.e., chains A and B and 1WEJ for Fab, i.e., chains D,E, F, G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 40% v/v PEG 400, 5% w/v PEG 3350, and 0.1 M acetic acid pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 3.49 64.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.48 α = 90 b = 145.48 β = 90 c = 216.334 γ = 90
Symmetry Space Group P 43 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 CCD MARMOSAIC 225 mm CCD 2010-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3.297 31.537 85009 30833
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 3ONU for P domain, i.e., chains A and B and 1WEJ for Fab, i.e., chains D,E, F, G 3.297 31.537 1 85009 30833 1532 86.38 0.2295 0.2268 0.2177 0.2826 0.275 Random
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] 5.8221 5.8221 -11.6441
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.842 f_angle_d 0.795 f_chiral_restr 0.054 f_bond_d 0.004 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11459 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASES phasing PHENIX refinement HKL-2000 data reduction SCALEPACK data scaling