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Crystallographic structure of apo porcine rotavirus TFR-41 VP8*
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I2S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M HEPES pH 7.4 and 2 M ammonium formate
Crystal Properties Matthews coefficient Solvent content 2.02 39.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.816 α = 90 b = 30.444 β = 124.05 c = 86.217 γ = 90
Symmetry Space Group C 1 2 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 CCD ADSC QUANTUM 315r 2014-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.954 Australian Synchrotron MX2
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 1.9 42.91 98.4 13 5.4 23031
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 89.5 0.148 2985
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2I2S 1.9 35.8 21861 1170 98.36 0.16616 0.16426 0.1738 0.20254 0.2134 RANDOM 12.564
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] 0.24 -0.08 -0.53 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.36 r_dihedral_angle_3_deg 10.241 r_dihedral_angle_4_deg 8.622 r_dihedral_angle_1_deg 6.324 r_long_range_B_refined 4.198 r_long_range_B_other 4.197 r_angle_refined_deg 1.228 r_scangle_other 1.068 r_mcangle_other 0.858 r_mcangle_it 0.857
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.36 r_dihedral_angle_3_deg 10.241 r_dihedral_angle_4_deg 8.622 r_dihedral_angle_1_deg 6.324 r_long_range_B_refined 4.198 r_long_range_B_other 4.197 r_angle_refined_deg 1.228 r_scangle_other 1.068 r_mcangle_other 0.858 r_mcangle_it 0.857 r_angle_other_deg 0.724 r_scbond_it 0.654 r_scbond_other 0.654 r_mcbond_it 0.505 r_mcbond_other 0.505 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2536 Nucleic Acid Atoms Solvent Atoms 336 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing