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Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine (8-oxoG)and dATP 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 2.36 47.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.33 α = 90 b = 79.61 β = 109.56 c = 55.83 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 2014-08-07 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 52.61 92.7 0.104 6.8 3.6 28674
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 2.05 90.8 0.562 2.2 3.2 6648
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 45.4 27220 1451 92.77 0.20923 0.20653 0.2128 0.2609 0.2619 RANDOM 33.646
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] -0.01 -0.16 0.27 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.63 r_dihedral_angle_4_deg 16.536 r_dihedral_angle_3_deg 14.712 r_long_range_B_refined 5.626 r_long_range_B_other 5.523 r_dihedral_angle_1_deg 5.038 r_scangle_other 3.495 r_mcangle_it 2.904 r_mcangle_other 2.903 r_scbond_it 2.113
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.63 r_dihedral_angle_4_deg 16.536 r_dihedral_angle_3_deg 14.712 r_long_range_B_refined 5.626 r_long_range_B_other 5.523 r_dihedral_angle_1_deg 5.038 r_scangle_other 3.495 r_mcangle_it 2.904 r_mcangle_other 2.903 r_scbond_it 2.113 r_scbond_other 2.112 r_mcbond_it 1.789 r_mcbond_other 1.788 r_angle_refined_deg 1.259 r_angle_other_deg 0.876 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 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 2604 Nucleic Acid Atoms 654 Solvent Atoms 202 Heterogen Atoms 14
Software Software Software Name Purpose PHASER phasing REFMAC refinement MOSFLM data reduction SCALEPACK data scaling