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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 MnCl2 for 35 s
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 2.14 42.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.85 α = 90 b = 82.29 β = 110.68 c = 54.68 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 2014-08-15 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 2.2 46.64 90.8 0.097 7.7 3.6 19135
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 2.27 90.1 0.604 2.3 3.5 5725
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 2.2 46.64 18209 926 90.93 0.19774 0.19404 0.1975 0.26868 0.2653 RANDOM 35.986
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 0.05 -0.07 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.819 r_dihedral_angle_3_deg 16.286 r_dihedral_angle_4_deg 12.511 r_long_range_B_refined 6.346 r_long_range_B_other 6.311 r_dihedral_angle_1_deg 5.986 r_scangle_other 4.176 r_mcangle_it 3.484 r_mcangle_other 3.483 r_scbond_other 2.617
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.819 r_dihedral_angle_3_deg 16.286 r_dihedral_angle_4_deg 12.511 r_long_range_B_refined 6.346 r_long_range_B_other 6.311 r_dihedral_angle_1_deg 5.986 r_scangle_other 4.176 r_mcangle_it 3.484 r_mcangle_other 3.483 r_scbond_other 2.617 r_scbond_it 2.616 r_mcbond_other 2.163 r_mcbond_it 2.162 r_angle_refined_deg 1.403 r_angle_other_deg 1.057 r_chiral_restr 0.089 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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 2682 Nucleic Acid Atoms 652 Solvent Atoms 155 Heterogen Atoms 34
Software Software Software Name Purpose PHASER phasing REFMAC refinement MOSFLM data reduction SCALEPACK data scaling