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Human DNA polymerase beta pre-catalytic 8-oxoG:dC extension complex with dTTP bound in Watson-Crick conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RPX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 50 mM imidazole pH 7.0-7.5, 350 mM sodium acetate, 16-18% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.27 45.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51 α = 90 b = 80.1 β = 107.2 c = 55.6 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 CCD RAYONIX MX300HE 2016-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.2 48.72 94.4 0.058 0.081 0.996 11.45 1.959 40358 -3 37.585
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.4 89.1 0.339 0.475 0.765 2.49 1.881
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4RPX 2.2 48.72 20062 1056 96.94 0.1905 0.1869 0.193 0.26 0.269 RANDOM 32.456
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] -0.29 -0.39 0.52 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.168 r_dihedral_angle_3_deg 16.724 r_dihedral_angle_4_deg 13.834 r_dihedral_angle_1_deg 6.034 r_angle_refined_deg 1.742 r_angle_other_deg 1.126 r_chiral_restr 0.097 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.168 r_dihedral_angle_3_deg 16.724 r_dihedral_angle_4_deg 13.834 r_dihedral_angle_1_deg 6.034 r_angle_refined_deg 1.742 r_angle_other_deg 1.126 r_chiral_restr 0.097 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2602 Nucleic Acid Atoms 632 Solvent Atoms 136 Heterogen Atoms 50
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data scaling PHASER phasing XDS data reduction