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Crystal structure of the rotavirus strain DS-1 VP8* core
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KQR PDB Entry 1KQR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 PEG 4000, sodium chloride, sodium citrate, ethanol, tris, EDTA, sodium azide, benzamidine, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.72 38.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.421 α = 90.03 b = 84.123 β = 90.02 c = 90.769 γ = 75.54
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 4 Mirrors 2003-02-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.9160 CHESS F1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 1.6 14.88 96.8 0.05 17.2 1.95 153466 153466 19.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.66 94.7 0.376 3.4 1.72 15018
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB Entry 1KQR 1.604 14.88 145697 145697 7761 100 0.15961 0.15961 0.1579 0.1771 0.19173 0.2058 RANDOM 24.907
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] 0.35 -0.06 0.07 -0.13 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.543 r_dihedral_angle_3_deg 11.706 r_dihedral_angle_4_deg 7.243 r_dihedral_angle_1_deg 6.684 r_scangle_it 2.495 r_scbond_it 1.789 r_angle_other_deg 1.506 r_angle_refined_deg 1.31 r_mcangle_it 1.019 r_mcbond_it 0.794
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.543 r_dihedral_angle_3_deg 11.706 r_dihedral_angle_4_deg 7.243 r_dihedral_angle_1_deg 6.684 r_scangle_it 2.495 r_scbond_it 1.789 r_angle_other_deg 1.506 r_angle_refined_deg 1.31 r_mcangle_it 1.019 r_mcbond_it 0.794 r_symmetry_vdw_other 0.205 r_nbd_refined 0.192 r_nbd_other 0.185 r_nbtor_refined 0.182 r_mcbond_other 0.177 r_symmetry_vdw_refined 0.165 r_symmetry_hbond_refined 0.151 r_xyhbond_nbd_refined 0.139 r_chiral_restr 0.084 r_nbtor_other 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10616 Nucleic Acid Atoms Solvent Atoms 1724 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling CNS refinement HKL-2000 data collection HKL-2000 data reduction CNS phasing