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Crystal structure of P[19] rotavirus VP8* complexed with LNFPI
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GJ6 PDB entry 5GJ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 295 0.5 M ammonium sulfate, 0.1 M sodium citrate tribasic dihydrate, pH 5.6, 1.0 M lithium sulfate monohydrate
Crystal Properties Matthews coefficient Solvent content 4.68 73.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.631 α = 90 b = 115.631 β = 90 c = 101.828 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX-225HE 2017-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.941 29.7 99.9 0.158 0.179 0.065 8.2 7.6 49456 49456
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.94 2.05 100 0.741 0.741 0.859 0.312 0.9 7.5 7204
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 5GJ6 1.94 29.7 47104 2417 99.92 0.2025 0.2012 0.2296 0.2245 RANDOM 26.043
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] -1.47 -1.47 2.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.64 r_dihedral_angle_4_deg 17.56 r_dihedral_angle_3_deg 13.785 r_dihedral_angle_1_deg 7.219 r_angle_refined_deg 1.439 r_angle_other_deg 0.74 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.64 r_dihedral_angle_4_deg 17.56 r_dihedral_angle_3_deg 13.785 r_dihedral_angle_1_deg 7.219 r_angle_refined_deg 1.439 r_angle_other_deg 0.74 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2562 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms 150
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction iMOSFLM data reduction PHASER phasing