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Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine(8-oxoG) and dCTP soaked with MgCl2 for 1hr
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RJE PDB entry 3RJE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 295 50 MM IMIDAZOLE, 350 MM SODIUM Acetate, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.38 48.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.42 α = 90 b = 80.3 β = 110.27 c = 55.8 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 193 CCD RAYONIX MX225HE 2014-08-06 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) 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 2.7 52.34 92.9 0.079 8.3 3.2 11818
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.83 92.5 0.426 2.1 3 4686
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 PDB entry 3RJE 2.7 45.63 11202 613 93.02 0.20737 0.20322 0.2056 0.28031 0.2815 RANDOM 60.551
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] -0.16 -0.09 0.48 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.457 r_dihedral_angle_3_deg 17.422 r_dihedral_angle_4_deg 14.089 r_long_range_B_refined 8.273 r_long_range_B_other 8.272 r_dihedral_angle_1_deg 6.203 r_scangle_other 5.574 r_mcangle_it 5.353 r_mcangle_other 5.352 r_scbond_other 3.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.457 r_dihedral_angle_3_deg 17.422 r_dihedral_angle_4_deg 14.089 r_long_range_B_refined 8.273 r_long_range_B_other 8.272 r_dihedral_angle_1_deg 6.203 r_scangle_other 5.574 r_mcangle_it 5.353 r_mcangle_other 5.352 r_scbond_other 3.54 r_scbond_it 3.539 r_mcbond_other 3.311 r_mcbond_it 3.31 r_angle_refined_deg 1.368 r_angle_other_deg 0.884 r_chiral_restr 0.065 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2598 Nucleic Acid Atoms 652 Solvent Atoms 10 Heterogen Atoms 6
Software Software Software Name Purpose PHASER phasing REFMAC refinement MOSFLM data reduction SCALEPACK data scaling