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Crystal structure of the human Wa rotavirus VP8* carbohydrate-recognising domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Homology model based on the structure of porcine CRW-8 VP8* that we have solved.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 295 25% PEG 4000, 20% 2-propanol, 0.1M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.07 59.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.762 α = 90 b = 74.762 β = 90 c = 70.09 γ = 120
Symmetry Space Group P 32 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 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 2.5 64.6 8135
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 Homology model based on the structure of porcine CRW-8 VP8* that we have solved. 2.5 64.55 2 8114 7491 355 96.54 0.17973 0.17718 0.173 0.23508 0.2369 RANDOM 31.888
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] 1.36 0.68 1.36 -2.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.678 r_dihedral_angle_3_deg 16.865 r_dihedral_angle_4_deg 12.765 r_dihedral_angle_1_deg 6.653 r_scangle_it 1.973 r_scbond_it 1.193 r_angle_refined_deg 1.106 r_mcangle_it 0.949 r_mcbond_it 0.528 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.678 r_dihedral_angle_3_deg 16.865 r_dihedral_angle_4_deg 12.765 r_dihedral_angle_1_deg 6.653 r_scangle_it 1.973 r_scbond_it 1.193 r_angle_refined_deg 1.106 r_mcangle_it 0.949 r_mcbond_it 0.528 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.206 r_nbd_refined 0.197 r_symmetry_hbond_refined 0.169 r_xyhbond_nbd_refined 0.115 r_chiral_restr 0.082 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1300 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XNEMO data collection FIP data collection MOSFLM data reduction CCP4 data scaling AMoRE phasing