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Crystallographic structure of apo human rotavirus K8 VP8*
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DRR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 2 M ammonium sulphate and 5% (v/v) isopropanol
Crystal Properties Matthews coefficient Solvent content 2.31 46.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.81 α = 90 b = 62.81 β = 90 c = 74.64 γ = 120
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 2012-11-27 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 1.8 54.4 100 5.3 10 15568
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 4DRR 1.8 54.39 14744 790 100 0.175 0.173 0.1729 0.216 0.2161 RANDOM 20.09
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] -0.53 -0.26 -0.53 1.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.374 r_dihedral_angle_3_deg 13.071 r_dihedral_angle_1_deg 6.61 r_dihedral_angle_4_deg 5.536 r_long_range_B_refined 5.348 r_scbond_it 1.668 r_mcangle_it 1.614 r_angle_refined_deg 1.309 r_mcbond_it 0.99 r_chiral_restr 0.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.374 r_dihedral_angle_3_deg 13.071 r_dihedral_angle_1_deg 6.61 r_dihedral_angle_4_deg 5.536 r_long_range_B_refined 5.348 r_scbond_it 1.668 r_mcangle_it 1.614 r_angle_refined_deg 1.309 r_mcbond_it 0.99 r_chiral_restr 0.097 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1295 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing