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Crystal Structure of Human DNA polymerase kappa in complex with DNA containing the major cisplatin lesion
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295.15 15-20% PEG400 and 0.1-0.2 M ammonium iodide (NH4I)
Crystal Properties Matthews coefficient Solvent content 2.58 52.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.69 α = 90 b = 129.06 β = 90 c = 168.088 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 RAYONIX MX-300 2014-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
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 2.8 48.47 99.6 0.093 0.996 9.7 4.4 36493
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.95 0.524 0.828 22702
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 2.8 48.47 34925 1405 99.37 0.21563 0.21359 0.2179 0.26895 0.2755 RANDOM 73.975
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] 10.33 -6.28 -4.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.176 r_dihedral_angle_4_deg 20.953 r_dihedral_angle_3_deg 16.443 r_long_range_B_refined 7.956 r_long_range_B_other 7.941 r_dihedral_angle_1_deg 5.161 r_mcangle_it 4.862 r_mcangle_other 4.861 r_scangle_other 4.601 r_mcbond_it 2.894
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.176 r_dihedral_angle_4_deg 20.953 r_dihedral_angle_3_deg 16.443 r_long_range_B_refined 7.956 r_long_range_B_other 7.941 r_dihedral_angle_1_deg 5.161 r_mcangle_it 4.862 r_mcangle_other 4.861 r_scangle_other 4.601 r_mcbond_it 2.894 r_mcbond_other 2.894 r_scbond_it 2.747 r_scbond_other 2.747 r_angle_refined_deg 1.22 r_angle_other_deg 1.188 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.004 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 6695 Nucleic Acid Atoms 896 Solvent Atoms 230 Heterogen Atoms 81
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling REFMAC phasing