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Cadmium 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 8.5 293 35% w/v 1,6-Hexanediol, 50 mM TRIS pH 8.5 75 mM Magnesium sulfate.
Crystal Properties Matthews coefficient Solvent content 2.2 44.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.471 α = 90 b = 43.471 β = 90 c = 83.887 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 6M 2023-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 2.0.1 1.03579 ALS 2.0.1
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 1.417 50 91.5 0.095 0.101 0.035 0.994 19.6 7.2 16509
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 1.42 1.44 56.4 0.286 0.35 0.198 0.834 3.4 2.4
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 1.417 41.944 16343 841 90.188 0.177 0.1749 0.1799 0.218 0.2241 12.69
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 -0.001 0.004
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 5.689 r_lrange_other 5.488 r_scangle_it 4.189 r_scangle_other 4.017 r_angle_other_deg 3.763 r_angle_refined_deg 2.868 r_scbond_it 2.586 r_scbond_other 2.317 r_chiral_restr_other 1.786 r_xyhbond_nbd_refined 0.333
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 5.689 r_lrange_other 5.488 r_scangle_it 4.189 r_scangle_other 4.017 r_angle_other_deg 3.763 r_angle_refined_deg 2.868 r_scbond_it 2.586 r_scbond_other 2.317 r_chiral_restr_other 1.786 r_xyhbond_nbd_refined 0.333 r_symmetry_nbtor_other 0.264 r_nbtor_refined 0.251 r_symmetry_xyhbond_nbd_refined 0.211 r_symmetry_nbd_other 0.192 r_nbd_other 0.182 r_chiral_restr 0.135 r_symmetry_nbd_refined 0.103 r_nbd_refined 0.084 r_dihedral_angle_other_2_deg 0.057 r_metal_ion_refined 0.036 r_bond_other_d 0.029 r_gen_planes_refined 0.022 r_bond_refined_d 0.019 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 644 Solvent Atoms 183 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing