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Structure of human DNA polymerase kappa inserting dATP opposite an 8-oxoG DNA lesion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OH2 PDB entry 2OH2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.3 277 14% PEG 5000 monomethyl ether, 0.2M potassium acetate, 0.1M sodium chloride, 0.1M sodium cacodylate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.63 66.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.846 α = 90 b = 154.48 β = 90 c = 217.293 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC QUANTUM 315 2005-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.100 NSLS X25
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 3.2 50 100 0.121 26.8 8.5 34388
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3.2 3.283 99.87 7.4 8.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB entry 2OH2 3.2 47.12 34388 31139 1640 99.93 0.22696 0.22453 0.2231 0.27403 0.2725 RANDOM 46.402
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] 3.18 1.33 -4.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.408 r_dihedral_angle_4_deg 21.503 r_dihedral_angle_3_deg 19.639 r_dihedral_angle_1_deg 5.589 r_scangle_it 2.131 r_angle_refined_deg 1.567 r_scbond_it 1.196 r_mcangle_it 0.979 r_angle_other_deg 0.964 r_mcbond_it 0.514
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.408 r_dihedral_angle_4_deg 21.503 r_dihedral_angle_3_deg 19.639 r_dihedral_angle_1_deg 5.589 r_scangle_it 2.131 r_angle_refined_deg 1.567 r_scbond_it 1.196 r_mcangle_it 0.979 r_angle_other_deg 0.964 r_mcbond_it 0.514 r_chiral_restr 0.069 r_mcbond_other 0.059 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6757 Nucleic Acid Atoms 1056 Solvent Atoms 18 Heterogen Atoms 64
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling