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Human DNA polymerase beta 8-oxoG:dC extension with dTTP after 20 s
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 2.26 45.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.9 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 2015-11-12 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 1.9 48.62 96.5 0.05 0.069 0.998 11.11 1.935 63931 -3 30.123
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 1.9 2.2 98.7 0.234 0.317 0.877 3.36 1.924
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 1.9 48.62 31519 1659 98.57 0.2048 0.2028 0.2088 0.2435 0.2478 RANDOM 27.365
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] 0.02 -0.04 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.361 r_dihedral_angle_4_deg 13.964 r_dihedral_angle_3_deg 13.482 r_dihedral_angle_1_deg 4.883 r_angle_refined_deg 1.148 r_angle_other_deg 1.021 r_chiral_restr 0.072 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.361 r_dihedral_angle_4_deg 13.964 r_dihedral_angle_3_deg 13.482 r_dihedral_angle_1_deg 4.883 r_angle_refined_deg 1.148 r_angle_other_deg 1.021 r_chiral_restr 0.072 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2617 Nucleic Acid Atoms 652 Solvent Atoms 305 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