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Hare calicivirus protruding domain and A-trisaccharide complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OR7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.2 M lithium sulfate, 0.1 M Bis-Tris, pH 5.5, 20% w/v PEG3350, 60-molar excess of A-trisaccharide
Crystal Properties Matthews coefficient Solvent content 2.46 50.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.11 α = 90 b = 82.526 β = 90.96 c = 74.331 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 X 9M 2024-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.95366 Australian Synchrotron MX1
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 1.42 44.62 99.6 0.069 0.998 6.9 4 123900
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 1.42 1.45 0.7
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 1.42 44.62 1.34 123900 1996 99.65 0.1556 0.1552 0.1552 0.1776 0.1776 22.33
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 6.4262 f_angle_d 1.0274 f_chiral_restr 0.0845 f_plane_restr 0.0108 f_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4830 Nucleic Acid Atoms Solvent Atoms 710 Heterogen Atoms 80
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing