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Structure of human DNA polymerase kappa with DNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295.15 25% PEG 400 and 0.2M ammonium iodide
Crystal Properties Matthews coefficient Solvent content 2.48 50.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.579 α = 90 b = 124.63 β = 90 c = 165.04 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 PIXEL DECTRIS EIGER X 16M 2017-07-31 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) Rrim I (All) 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 44.14 98.3 0.07 0.079 0.998 12 4.5 93082
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 2.11 97.4 0.55 0.88 2.8 4.7
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 44.14 90700 2327 98.05 0.19923 0.19833 0.2044 0.23416 0.2393 RANDOM 41.577
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] 4.99 -1.65 -3.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.54 r_dihedral_angle_4_deg 19.345 r_dihedral_angle_3_deg 16.035 r_long_range_B_refined 7.584 r_long_range_B_other 7.549 r_dihedral_angle_1_deg 5.729 r_scangle_other 5.572 r_mcangle_it 4.036 r_mcangle_other 4.036 r_scbond_it 3.614
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.54 r_dihedral_angle_4_deg 19.345 r_dihedral_angle_3_deg 16.035 r_long_range_B_refined 7.584 r_long_range_B_other 7.549 r_dihedral_angle_1_deg 5.729 r_scangle_other 5.572 r_mcangle_it 4.036 r_mcangle_other 4.036 r_scbond_it 3.614 r_scbond_other 3.614 r_mcbond_it 2.695 r_mcbond_other 2.694 r_angle_refined_deg 1.532 r_angle_other_deg 1.072 r_chiral_restr 0.095 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.003 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 6979 Nucleic Acid Atoms 898 Solvent Atoms 483 Heterogen Atoms 168
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing