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Pre-catalytic ternary complex of Human DNA Polymerase Beta With Gapped DNA substrate incoming (-)3TC-TP and Ca2+.
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
Crystal Properties Matthews coefficient Solvent content 2.35 47.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.63 α = 90 b = 79.45 β = 106.66 c = 55.17 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 295 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 2.2 44.03 99.9 0.16 6.2 3.6 23005
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 2.27 100 0.442 4.6 3.4
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 2.3 44.03 19157 997 99.9 0.233 0.23 0.235 0.284 0.2882 RANDOM 39.93
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] 0.09 -0.03 0.03 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.845 r_dihedral_angle_4_deg 17.52 r_dihedral_angle_3_deg 16.39 r_long_range_B_refined 7.219 r_long_range_B_other 7.208 r_dihedral_angle_1_deg 6.257 r_mcangle_it 4.404 r_mcangle_other 4.404 r_scangle_other 3.975 r_mcbond_it 2.695
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.845 r_dihedral_angle_4_deg 17.52 r_dihedral_angle_3_deg 16.39 r_long_range_B_refined 7.219 r_long_range_B_other 7.208 r_dihedral_angle_1_deg 6.257 r_mcangle_it 4.404 r_mcangle_other 4.404 r_scangle_other 3.975 r_mcbond_it 2.695 r_mcbond_other 2.664 r_scbond_it 2.493 r_scbond_other 2.492 r_angle_refined_deg 1.476 r_angle_other_deg 0.946 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_bond_other_d 0.007 r_gen_planes_refined 0.006 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 2612 Nucleic Acid Atoms 632 Solvent Atoms 94 Heterogen Atoms 56
Software Software Software Name Purpose MOSFLM data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement