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Human DNA polymerase beta crosslinked ternary complex with Sp-dCTP-alpha-S
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7RBH Human DNA polymerase beta crosslinked ternary complex 2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 0.1 M Sodium Citrate pH 5.5, 18% PEG6000
Crystal Properties Matthews coefficient Solvent content 2 45.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.683 α = 90 b = 77.875 β = 105.627 c = 54.778 γ = 90
Symmetry Space Group P 1 21 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 2025-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.1 45.92 90.8 0.09 1 9.6 3.8 20468
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 0.09 1
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.1 45.92 20466 1099 90.574 0.207 0.2041 0.2045 0.2566 0.2573 RANDOM 59.513
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] 0.106 -0.008 0.061 -0.141
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.452 r_dihedral_angle_6_deg 14.701 r_lrange_it 10.619 r_dihedral_angle_2_deg 9.739 r_scangle_it 8.881 r_mcangle_it 7.079 r_dihedral_angle_1_deg 6.727 r_scbond_it 6.135 r_mcbond_it 4.878 r_angle_refined_deg 1.682
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.452 r_dihedral_angle_6_deg 14.701 r_lrange_it 10.619 r_dihedral_angle_2_deg 9.739 r_scangle_it 8.881 r_mcangle_it 7.079 r_dihedral_angle_1_deg 6.727 r_scbond_it 6.135 r_mcbond_it 4.878 r_angle_refined_deg 1.682 r_nbtor_refined 0.314 r_nbd_refined 0.237 r_metal_ion_refined 0.195 r_symmetry_nbd_refined 0.174 r_xyhbond_nbd_refined 0.161 r_chiral_restr 0.109 r_symmetry_xyhbond_nbd_refined 0.106 r_gen_planes_refined 0.007 r_bond_refined_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2438 Nucleic Acid Atoms 631 Solvent Atoms 28 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing Coot model building