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Precatalytic ternary complex of Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine (8-oxoG) and dCTP in the presence of CaCl2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KLD PDB entry 4KLD
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 2.16 43.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.66 α = 90 b = 79.36 β = 106.34 c = 55.65 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 2014-06-20 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 1.9 31.85 95.4 0.083 6.8 3.3 31220
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 1.9 1.94 91.6 0.37 2 3.1 5883
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 4KLD 1.9 31.43 29702 1517 95.45 0.1907 0.18886 0.1963 0.22667 0.2316 RANDOM 24.155
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] -0.07 0.05 -0.01 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.171 r_dihedral_angle_4_deg 14.291 r_dihedral_angle_3_deg 13.415 r_dihedral_angle_1_deg 5.091 r_long_range_B_refined 4.217 r_long_range_B_other 4.128 r_scangle_other 2.171 r_mcangle_it 2.043 r_mcangle_other 2.042 r_scbond_it 1.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.171 r_dihedral_angle_4_deg 14.291 r_dihedral_angle_3_deg 13.415 r_dihedral_angle_1_deg 5.091 r_long_range_B_refined 4.217 r_long_range_B_other 4.128 r_scangle_other 2.171 r_mcangle_it 2.043 r_mcangle_other 2.042 r_scbond_it 1.304 r_scbond_other 1.304 r_angle_refined_deg 1.283 r_mcbond_it 1.194 r_mcbond_other 1.192 r_angle_other_deg 1.048 r_chiral_restr 0.075 r_bond_refined_d 0.006 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 2613 Nucleic Acid Atoms 633 Solvent Atoms 246 Heterogen Atoms 80
Software Software Software Name Purpose PHASER phasing REFMAC refinement MOSFLM data reduction SCALEPACK data scaling