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Postcatalytic ternary complex of Human DNA Polymerase Beta with Gapped DNA substrate, incorporated (-)FTC and PPi.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RQ7
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,
Crystal Properties Matthews coefficient Solvent content 2.38 48.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.17 α = 90 b = 79.33 β = 107.2 c = 55.46 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 2014-12-03 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 2.39 44.52 99.9 0.094 7.7 3.6 18179
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 2.39 2.48 100 0.474 2 3.3
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 4RQ7 2.39 44.52 17190 968 99.8 0.216 0.213 0.2174 0.269 0.272 RANDOM 41.67
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] -0.21 -0.01 0.04 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.126 r_dihedral_angle_3_deg 16.301 r_dihedral_angle_4_deg 9.361 r_long_range_B_refined 7.263 r_long_range_B_other 7.263 r_dihedral_angle_1_deg 5.793 r_scangle_other 5.055 r_mcangle_other 4.916 r_mcangle_it 4.914 r_scbond_it 3.395
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.126 r_dihedral_angle_3_deg 16.301 r_dihedral_angle_4_deg 9.361 r_long_range_B_refined 7.263 r_long_range_B_other 7.263 r_dihedral_angle_1_deg 5.793 r_scangle_other 5.055 r_mcangle_other 4.916 r_mcangle_it 4.914 r_scbond_it 3.395 r_scbond_other 3.394 r_mcbond_it 3.116 r_mcbond_other 3.088 r_angle_refined_deg 1.535 r_angle_other_deg 0.926 r_chiral_restr 0.08 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 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 2368 Nucleic Acid Atoms 632 Solvent Atoms 35 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALEPACK data scaling PHASER phasing