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Crystal Structure of the porcine CRW-8 rotavirus VP8* carbohydrate-recognising domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other Homology model based on the structure of Rhesus rotavirus VP8*
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 70% MPD, 0.1M HEPES pH 7.5, methyl-alpha-D-N-acetylneuraminide , VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.59 52.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.929 α = 90 b = 64.663 β = 90 c = 109.886 γ = 90
Symmetry Space Group P 21 21 21
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 MAR CCD 165 mm mirrors 2004-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.9794 ESRF BM30A
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 2.3 55.9 17704
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 Homology model based on the structure of Rhesus rotavirus VP8* 2.3 20 17658 16756 901 99.77 0.183 0.1654 0.16256 0.21952 0.182 RANDOM 21.243
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 1.74 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.637 r_dihedral_angle_3_deg 12.934 r_dihedral_angle_4_deg 10.175 r_dihedral_angle_1_deg 6.108 r_scangle_it 1.43 r_angle_refined_deg 1.06 r_scbond_it 0.892 r_mcangle_it 0.593 r_nbtor_refined 0.306 r_mcbond_it 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.637 r_dihedral_angle_3_deg 12.934 r_dihedral_angle_4_deg 10.175 r_dihedral_angle_1_deg 6.108 r_scangle_it 1.43 r_angle_refined_deg 1.06 r_scbond_it 0.892 r_mcangle_it 0.593 r_nbtor_refined 0.306 r_mcbond_it 0.306 r_nbd_refined 0.187 r_symmetry_hbond_refined 0.159 r_symmetry_vdw_refined 0.138 r_xyhbond_nbd_refined 0.123 r_metal_ion_refined 0.08 r_chiral_restr 0.063 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2606 Nucleic Acid Atoms Solvent Atoms 363 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement XNEWMO data collection FIP data collection MOSFLM data reduction CCP4 data scaling AMoRE phasing