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Structure of human DNA polymerase kappa in complex with Lucidin-derived DNA adduct and incoming dCMPNPP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295.15 25-30% PEG400, 0.2M ammonium nitrate
Crystal Properties Matthews coefficient Solvent content 2.45 49.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.891 α = 90 b = 129.014 β = 90 c = 167.346 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2017-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.9792 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.9 47.25 99.2 0.056 0.999 14.8 4.8 31180
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3.06 99.8 0.578 0.903 2.5 5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 2.9 47.25 29905 1228 98.94 0.23261 0.23104 0.231 0.26956 0.2626 RANDOM 109.151
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] 22.31 -13.78 -8.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.115 r_dihedral_angle_4_deg 19.582 r_dihedral_angle_3_deg 16.118 r_long_range_B_refined 13.745 r_long_range_B_other 13.745 r_scangle_other 9.706 r_mcangle_it 9.345 r_mcangle_other 9.344 r_scbond_it 6.011 r_scbond_other 6.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.115 r_dihedral_angle_4_deg 19.582 r_dihedral_angle_3_deg 16.118 r_long_range_B_refined 13.745 r_long_range_B_other 13.745 r_scangle_other 9.706 r_mcangle_it 9.345 r_mcangle_other 9.344 r_scbond_it 6.011 r_scbond_other 6.01 r_mcbond_it 5.93 r_mcbond_other 5.93 r_dihedral_angle_1_deg 5.723 r_angle_refined_deg 1.388 r_angle_other_deg 1.198 r_chiral_restr 0.102 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.005 r_gen_planes_other 0.003 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 6663 Nucleic Acid Atoms 942 Solvent Atoms 28 Heterogen Atoms 102
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling REFMAC phasing