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Crystal structure of Caenorhabditis elegans Dicer-related helicase 3 (DRH-3) N-terminal domain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 277.15 0.2 M ammonium fluoride (pH 6.2), 20% w/v polyethylene glycol 3350, 5 mM dithiothreitol
Crystal Properties Matthews coefficient Solvent content 2.96 58.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.18 α = 90 b = 93.18 β = 90 c = 215.958 γ = 90
Symmetry Space Group P 41 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 100 PIXEL DECTRIS PILATUS 2M-F 2015-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.9998 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.8 85.56 99.3 0.134 0.146 0.996 10.9 11.1 24012 66.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.95 99 0.896 0.992 0.752 2.2 10.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.8 70.64 22582 1201 98.03 0.23632 0.23374 0.2344 0.28597 0.2853 RANDOM 80.548
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] -0.32 -0.32 0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.488 r_dihedral_angle_3_deg 19.875 r_dihedral_angle_4_deg 17.838 r_long_range_B_other 14.495 r_mcangle_it 9.651 r_mcangle_other 9.65 r_scangle_other 9.174 r_mcbond_it 6.474 r_mcbond_other 6.473 r_scbond_it 5.895
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.488 r_dihedral_angle_3_deg 19.875 r_dihedral_angle_4_deg 17.838 r_long_range_B_other 14.495 r_mcangle_it 9.651 r_mcangle_other 9.65 r_scangle_other 9.174 r_mcbond_it 6.474 r_mcbond_other 6.473 r_scbond_it 5.895 r_scbond_other 5.895 r_dihedral_angle_1_deg 5.262 r_angle_refined_deg 1.188 r_angle_other_deg 1.139 r_chiral_restr 0.053 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5218 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling Auto-Rickshaw phasing