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THE STRUCTURE OF PARIACOTO VIRUS REVEALS A DODECAHEDRAL CAGE OF DUPLEX RNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other crystal structure of flock house virus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 PEG 8000, lithium sulphate, calcium chloride, Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 329.332 α = 90 b = 346.944 β = 90.83 c = 424.893 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 CCD OTHER 1999-11-14 M SINGLE WAVELENGTH 2 1 90 CCD OTHER 1999-04-22
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 SSRL BL9-2 2 SYNCHROTRON APS BEAMLINE 14-ID-B APS 14-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 3 207 81.2 0.105 8.9 2.14 1505825 1505825 28
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) 3 3.05 82.2 0.266 3.3 1.79 76058
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 and electron density averaging throughtout crystal structure of flock house virus 3 20 3 1464339 1237980 123840 65.6 0.218 0.219 0.2351 0.221 0.2351 RANDOM 33.8
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]
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 27.8 x_scangle_it 2.76 x_mcangle_it 2.17 x_scbond_it 1.74 x_angle_deg 1.4 x_mcbond_it 1.21 x_improper_angle_d 0.8 x_bond_d 0.008 x_bond_d_na x_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 27.8 x_scangle_it 2.76 x_mcangle_it 2.17 x_scbond_it 1.74 x_angle_deg 1.4 x_mcbond_it 1.21 x_improper_angle_d 0.8 x_bond_d 0.008 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na x_angle_deg_prot x_dihedral_angle_d_na x_dihedral_angle_d_prot x_improper_angle_d_na x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7985 Nucleic Acid Atoms 509 Solvent Atoms 219 Heterogen Atoms 6
Software Software Software Name Purpose GLRF phasing X-PLOR model building X-PLOR refinement DENZO data reduction SCALEPACK data scaling X-PLOR phasing