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Magnesium catalyzed primer extension product with 14mer primer and mixed phosphorothioate activated G monomer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5L00
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 2.5 M Sodium chloride, 50 mM TRIS pH 7.5, 0.25 M Magnesium chloride.
Crystal Properties Matthews coefficient Solvent content 2.19 43.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.57 α = 90 b = 43.57 β = 90 c = 84.342 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 PILATUS3 2M 2023-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.97648 ALS 5.0.3
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 1.25 50 98.4 0.044 0.042 0.014 0.989 50.2 8.4 27390
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 1.25 1.27 82 0.424 0.499 0.255 0.842 2.9 3.5
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 NONE 1.25 37.733 24841 1156 94.034 0.188 0.1878 0.192 0.1908 0.1973 13.775
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] 0.001 0.001 -0.003
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 5.495 r_lrange_other 5.16 r_scangle_it 3.753 r_scangle_other 3.752 r_angle_other_deg 3.468 r_scbond_it 2.935 r_scbond_other 2.934 r_angle_refined_deg 2.926 r_chiral_restr_other 1.693 r_xyhbond_nbd_refined 0.273
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 5.495 r_lrange_other 5.16 r_scangle_it 3.753 r_scangle_other 3.752 r_angle_other_deg 3.468 r_scbond_it 2.935 r_scbond_other 2.934 r_angle_refined_deg 2.926 r_chiral_restr_other 1.693 r_xyhbond_nbd_refined 0.273 r_symmetry_nbtor_other 0.265 r_nbtor_refined 0.247 r_symmetry_nbd_other 0.204 r_nbd_refined 0.189 r_symmetry_xyhbond_nbd_refined 0.178 r_nbd_other 0.167 r_symmetry_nbd_refined 0.122 r_chiral_restr 0.119 r_dihedral_angle_other_2_deg 0.079 r_bond_other_d 0.028 r_gen_planes_refined 0.024 r_bond_refined_d 0.022 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 690 Solvent Atoms 165 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing