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Precatalytic ternary complex of Human DNA Polymerase Beta in closed conformation With Gapped DNA substrate incoming (-)3TC-TP and Mn2+.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RPX
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 2.08 40.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.48 α = 90 b = 81.4 β = 110.28 c = 53.57 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 46.41 98.2 0.109 6.4 3.3 26398
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 97.6 0.433 2 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 4RPX 2 46.41 25091 1287 97.7 0.184 0.182 0.1874 0.23 0.2329 RANDOM 22.35
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] 0.05 -0.05 -0.04 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.394 r_dihedral_angle_4_deg 15.121 r_dihedral_angle_3_deg 14.664 r_dihedral_angle_1_deg 6.392 r_long_range_B_refined 5.385 r_long_range_B_other 5.348 r_scangle_other 3.733 r_mcangle_it 2.602 r_mcangle_other 2.601 r_scbond_it 2.452
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.394 r_dihedral_angle_4_deg 15.121 r_dihedral_angle_3_deg 14.664 r_dihedral_angle_1_deg 6.392 r_long_range_B_refined 5.385 r_long_range_B_other 5.348 r_scangle_other 3.733 r_mcangle_it 2.602 r_mcangle_other 2.601 r_scbond_it 2.452 r_scbond_other 2.452 r_angle_refined_deg 1.696 r_mcbond_it 1.646 r_mcbond_other 1.63 r_angle_other_deg 1.137 r_chiral_restr 0.099 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 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 2639 Nucleic Acid Atoms 632 Solvent Atoms 201 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALA data scaling PHASER phasing