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Structure of C. elegans Dicer-related helicase 1 (DRH1) bound to blunt end 5'P-dsRNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5E3H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 Directly after size exclusion chromatography DRH-1deltaN_E431Q was concentrated 10 mg/ml and mixed with 12 dsRNAp in a 1:2 molar ratio, ADP-AlF4 (adenosine-5-diphosphate with aluminium fluoride) and 2 mM MgCl2 were added then incubated for 30 minutes on ice. The complex was mixed with reservoir buffer (0.2 M tri Ammonium citrate 20 % PEG3350 or 0.2 M Sodium malonate dibasic monohydrate 20% PEG3350) in 1:1 ratio. Crystals grew in two weeks at 4 C.
Crystal Properties Matthews coefficient Solvent content 2.62 53.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.354 α = 90 b = 134.354 β = 90 c = 221.301 γ = 90
Symmetry Space Group I 41 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 100 PIXEL DECTRIS PILATUS 6M 2016-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97931 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.18 114.846 84.2 0.075 0.087 0.037 0.999 11 5 44595
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.18 2.335 23 1.549 0.514 1.5 5.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.18 72.08 1.35 44588 2277 84.21 0.2199 0.2179 0.2177 0.2569 0.257 85.19
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 f_dihedral_angle_d 14.9177 f_angle_d 0.5001 f_chiral_restr 0.0387 f_plane_restr 0.0044 f_bond_d 0.0027
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5584 Nucleic Acid Atoms 748 Solvent Atoms 80 Heterogen Atoms 28
Software Software Software Name Purpose PHENIX refinement autoPROC data reduction STARANISO data scaling MOLREP phasing