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Crystal structure of Tomato Aspermy Virus 2b in complex with siRNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5 293 20% PEG 4000, 0.2 M ammonium sulfate, 0.1 M sodium acetate, pH 5.0, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.94 58.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.9 α = 90 b = 165.67 β = 90 c = 35.59 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 200 CCD ADSC QUANTUM 315 2006-10-19 M MAD 2 1 x-ray 200 CCD ADSC QUANTUM 315 2006-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97907, 0.97927, 0.96411 APS 24-ID-C 2 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97918 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1,2 3.2 50 87.9 0.09 0.09 10.7 5.9 12056 10597 2 2
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) 3.2 3.31 69.6 0.574 0.574 2.6 5.4 803
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 MAD THROUGHOUT 3.23 50 12056 7907 755 65 0.231 0.226 0.2189 0.274 0.2674 RANDOM 106.986
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] -0.84 0.65 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.467 r_dihedral_angle_3_deg 20.88 r_dihedral_angle_4_deg 19.506 r_dihedral_angle_1_deg 4.758 r_angle_refined_deg 1.467 r_scangle_it 1.051 r_mcangle_it 0.907 r_scbond_it 0.546 r_mcbond_it 0.49 r_nbtor_refined 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.467 r_dihedral_angle_3_deg 20.88 r_dihedral_angle_4_deg 19.506 r_dihedral_angle_1_deg 4.758 r_angle_refined_deg 1.467 r_scangle_it 1.051 r_mcangle_it 0.907 r_scbond_it 0.546 r_mcbond_it 0.49 r_nbtor_refined 0.29 r_symmetry_hbond_refined 0.223 r_nbd_refined 0.22 r_symmetry_vdw_refined 0.21 r_xyhbond_nbd_refined 0.182 r_chiral_restr 0.12 r_bond_refined_d 0.007 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1926 Nucleic Acid Atoms 3240 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHELX phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection SHELXD phasing