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RNA primer non-enzymatic extension product with RNA substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6C8O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 0.05 M HEPES pH 7.0, 0.2 M Ammonium acetate, 0.15 M Magnesium acetate, 10% w/v Polyethylene glycol 6,000
Crystal Properties Matthews coefficient Solvent content 2.77 55.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.338 α = 90 b = 47.338 β = 90 c = 83.136 γ = 120
Symmetry Space Group P 3 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 99 PIXEL DECTRIS EIGER X 16M 2022-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033175 APS 23-ID-B
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 1.592 50 99.3 0.058 0.062 0.022 0.982 37.2 8.4 14954
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.592 1.63 88.8 0.336 0.366 0.139 0.993 5.5 5.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.592 41.568 12475 682 82.979 0.227 0.2264 0.2288 0.2474 0.2491 16.911
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] -0.005 -0.002 -0.005 0.015
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 6.825 r_lrange_other 6.638 r_scangle_it 4.375 r_scangle_other 4.373 r_angle_other_deg 3.642 r_angle_refined_deg 2.968 r_scbond_it 2.726 r_scbond_other 2.725 r_chiral_restr_other 1.927 r_chiral_restr 0.446
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 6.825 r_lrange_other 6.638 r_scangle_it 4.375 r_scangle_other 4.373 r_angle_other_deg 3.642 r_angle_refined_deg 2.968 r_scbond_it 2.726 r_scbond_other 2.725 r_chiral_restr_other 1.927 r_chiral_restr 0.446 r_nbtor_refined 0.248 r_xyhbond_nbd_refined 0.231 r_symmetry_nbtor_other 0.223 r_symmetry_xyhbond_nbd_refined 0.214 r_symmetry_nbd_other 0.206 r_symmetry_nbd_refined 0.174 r_nbd_other 0.173 r_metal_ion_refined 0.119 r_nbd_refined 0.102 r_dihedral_angle_other_2_deg 0.085 r_bond_other_d 0.024 r_bond_refined_d 0.022 r_gen_planes_refined 0.016 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 644 Solvent Atoms 132 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing