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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 20-25% PEG5KMME and 0.1-0.2M ammonium iodide
Crystal Properties Matthews coefficient Solvent content 2.45 49.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.8 α = 90 b = 127.72 β = 90 c = 168.14 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 2016-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.9801 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 3.15 41.27 93.7 0.101 0.996 8 3.6 23000
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 3.15 3.32 0.55 0.791 13039
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 3.15 41.27 21552 1216 92.86 0.24705 0.2442 0.2453 0.29851 0.2987 RANDOM 82.172
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] 13.29 -9.27 -4.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.371 r_dihedral_angle_4_deg 17.044 r_dihedral_angle_3_deg 16.705 r_long_range_B_refined 8.62 r_long_range_B_other 8.619 r_dihedral_angle_1_deg 5.827 r_mcangle_it 5.534 r_mcangle_other 5.533 r_scangle_other 5.484 r_scbond_it 3.651
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.371 r_dihedral_angle_4_deg 17.044 r_dihedral_angle_3_deg 16.705 r_long_range_B_refined 8.62 r_long_range_B_other 8.619 r_dihedral_angle_1_deg 5.827 r_mcangle_it 5.534 r_mcangle_other 5.533 r_scangle_other 5.484 r_scbond_it 3.651 r_scbond_other 3.651 r_mcbond_it 3.416 r_mcbond_other 3.416 r_angle_refined_deg 1.332 r_angle_other_deg 1.026 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 6573 Nucleic Acid Atoms 890 Solvent Atoms 25 Heterogen Atoms 81
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling REFMAC phasing