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The Atomic Structure of Rice dwarf Virus (RDV)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Cryo-electronmicrograph
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 His-Mg buffer, MgCl2, PEG8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 770 α = 90 b = 795 β = 90 c = 814 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 285 DIFFRACTOMETER WEISSENBERG Fused quartz mirror 1998-10-14 M SINGLE WAVELENGTH 2 1 x-ray 285 DIFFRACTOMETER WEISSENBERG Pt-coated quartz mirror 1998-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 1.0 Photon Factory BL-6A 2 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6B 1.0 Photon Factory BL-6B
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 1,2 3.5 230 97.7 0.186 3.1 5.9 3072898 3072898 41.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 3.5 3.59 91.5 0.783 0.783 0.9 2.8
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION Molecular Replacement Averaging THROUGHOUT Cryo-electronmicrograph 3.5 228.74 3072895 2772912 138283 90.1 0.303 0.303 0.303 0.306 random 39.5
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 c_dihedral_angle_d 23.2 c_scangle_it 3.19 c_mcangle_it 2.59 c_scbond_it 1.86 c_angle_deg 1.5 c_mcbond_it 1.43 c_improper_angle_d 0.91 c_bond_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 58130 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALA data scaling RAVE model building CCP4 model building other jiffy programs model building CNS refinement CCP4 data scaling RAVE phasing CCP4 phasing