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Human DNA polymerase beta pre-catalytic 8-oxoG:dA 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 2.28 46.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.94 α = 90 b = 80.49 β = 107.28 c = 55.66 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 2016-04-01 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) 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 2.33 53.15 99.7 0.071 0.084 0.045 0.99 12.4 3.3 18374
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 2.33 2.41 99.9 0.18 0.214 0.115 0.946 3.3
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 2.33 48.64 17477 879 99.68 0.1904 0.1874 0.1946 0.2498 0.2525 RANDOM 25.526
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] 0.03 -0.02 0.04 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.148 r_dihedral_angle_3_deg 16.595 r_dihedral_angle_4_deg 15.305 r_dihedral_angle_1_deg 6.064 r_angle_refined_deg 1.614 r_angle_other_deg 1.126 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.148 r_dihedral_angle_3_deg 16.595 r_dihedral_angle_4_deg 15.305 r_dihedral_angle_1_deg 6.064 r_angle_refined_deg 1.614 r_angle_other_deg 1.126 r_chiral_restr 0.09 r_bond_refined_d 0.012 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 2600 Nucleic Acid Atoms 634 Solvent Atoms 147 Heterogen Atoms 34
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction PHASER phasing