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Crystal structure of RNA silencing suppressor p19 complexed with double-helical RNA 20mer pG(CUG)6C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R9F PDB ENTRY 1R9F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 291 1.6 M ammonium sulfate, pH 8, potassium chloride, MES/NaOH, trace magnesium, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.77 55.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.917 α = 90 b = 89.917 β = 90 c = 148.353 γ = 120
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 315r M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.98035 ESRF ID23-1
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 1.95 20 98.9 0.072 11 2.9 32588 32285
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) 1 1.95 2.02 98.2 0.726 2.9 1628
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 PDB ENTRY 1R9F 1.95 19.3 30613 1632 99.19 0.1981 0.1962 0.2003 0.2342 0.24 RANDOM 36.6245
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] 12.18 12.18 -24.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.853 r_dihedral_angle_4_deg 21.029 r_dihedral_angle_3_deg 14.987 r_dihedral_angle_1_deg 5.757 r_mcangle_it 3.006 r_mcbond_other 2.199 r_mcbond_it 2.198 r_angle_refined_deg 2.032 r_angle_other_deg 1.445 r_chiral_restr 0.209
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.853 r_dihedral_angle_4_deg 21.029 r_dihedral_angle_3_deg 14.987 r_dihedral_angle_1_deg 5.757 r_mcangle_it 3.006 r_mcbond_other 2.199 r_mcbond_it 2.198 r_angle_refined_deg 2.032 r_angle_other_deg 1.445 r_chiral_restr 0.209 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d 0.006 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2004 Nucleic Acid Atoms 844 Solvent Atoms 223 Heterogen Atoms 22
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction REFMAC phasing