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Structure of Human pir-miRNA-340 Apical Loop and One-base-pair Fused to the YdaO Riboswitch Scaffold
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QK8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 297 1.89 M (NH4)2SO4, 0.214 M Li2SO4, and 0.1 M HEPES pH 7.4
Crystal Properties Matthews coefficient Solvent content 5.34 76.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.8 α = 90 b = 114.8 β = 90 c = 115.57 γ = 120
Symmetry Space Group P 31 2 1
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 PILATUS3 S 6M 2017-12-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.116 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.991 75.369 99.9 0.101 0.016 1 27.1 38.2 18192
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.991 3.1 100 2.02 0.324 0.848 2.4 35.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 THROUGHOUT 4QK8 2.991 75.369 1.36 18192 1818 99.87 0.1543 0.1514 0.155 0.1806 0.1839 113.5714
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 17.034 f_angle_d 1.059 f_chiral_restr 0.046 f_bond_d 0.005 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 2722 Solvent Atoms 4 Heterogen Atoms 98
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHENIX phasing