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Postcatalytic ternary complex of Human DNA Polymerase Beta with Gapped DNA substrate, incorporated (-)3TC 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 2.34 47.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.697 α = 90 b = 79.325 β = 107.03 c = 54.947 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 2013-10-11 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 2.49 25.18 99.6 0.168 11.9 5.6 15629
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 2.5 2.59 100 0.708 5.8
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 2.49 25.18 14831 781 99.1 0.208 0.205 0.2085 0.273 0.2717 RANDOM 41.5
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] -0.14 -0.12 0.06 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.345 r_dihedral_angle_4_deg 19.166 r_dihedral_angle_3_deg 16.114 r_long_range_B_other 6.752 r_long_range_B_refined 6.75 r_dihedral_angle_1_deg 6.516 r_mcangle_it 4.632 r_mcangle_other 4.631 r_scangle_other 4.247 r_mcbond_other 2.782
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.345 r_dihedral_angle_4_deg 19.166 r_dihedral_angle_3_deg 16.114 r_long_range_B_other 6.752 r_long_range_B_refined 6.75 r_dihedral_angle_1_deg 6.516 r_mcangle_it 4.632 r_mcangle_other 4.631 r_scangle_other 4.247 r_mcbond_other 2.782 r_mcbond_it 2.781 r_scbond_it 2.735 r_scbond_other 2.735 r_angle_refined_deg 1.464 r_angle_other_deg 0.897 r_chiral_restr 0.074 r_bond_refined_d 0.01 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 2537 Nucleic Acid Atoms 632 Solvent Atoms 59 Heterogen Atoms 32
Software Software Software Name Purpose HKL-2000 data reduction SCALA data scaling PHASER phasing REFMAC refinement