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Pre-catalytic ternary complex of Human DNA Polymerase Beta With Gapped DNA substrate incoming (-)FTC-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 2.32 47.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.615 α = 90 b = 79.395 β = 107.6 c = 54.795 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 1.79 15.78 99.3 0.069 19.75 5.6 41380
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 1.8 1.86 100 0.778 2.46 5.6
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 1.79 15.78 39217 2076 99 0.202 0.2 0.208 0.247 0.2507 RANDOM 44.31
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] -0.44 0.34 -0.46 0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.13 r_dihedral_angle_4_deg 14.289 r_dihedral_angle_3_deg 13.716 r_long_range_B_refined 6.621 r_long_range_B_other 6.549 r_dihedral_angle_1_deg 5.85 r_scangle_other 4.564 r_mcangle_it 3.972 r_mcangle_other 3.972 r_scbond_it 3.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.13 r_dihedral_angle_4_deg 14.289 r_dihedral_angle_3_deg 13.716 r_long_range_B_refined 6.621 r_long_range_B_other 6.549 r_dihedral_angle_1_deg 5.85 r_scangle_other 4.564 r_mcangle_it 3.972 r_mcangle_other 3.972 r_scbond_it 3.001 r_scbond_other 3.001 r_mcbond_it 2.747 r_mcbond_other 2.741 r_angle_refined_deg 1.458 r_angle_other_deg 1.105 r_chiral_restr 0.092 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 2592 Nucleic Acid Atoms 632 Solvent Atoms 242 Heterogen Atoms 46
Software Software Software Name Purpose HKL-2000 data reduction SCALA data scaling PHASER phasing REFMAC refinement