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Structure and Activity of Bypass Synthesis by Human DNA Polymerase Kappa Opposite the 7,8-Dihydro-8-oxodeoxyguanosine Adduct
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 7 175 MM NACL, 25 MM HEPES PH 7.3, 5 MM GLYCEROL, 2.5 MM 2-MERCHAPTOETHANOL, 0.5 MM TECEP, 5 MM CACL2, 5 MM DGTP, 9% PEG5000MME, 0.1 M AMMONIUM ACETATE, 10 MM MES PH 6.5
Crystal Properties Matthews coefficient Solvent content 4.4 74.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 165.482 α = 90 b = 217.629 β = 90 c = 117.957 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 MARRESEARCH 2007-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 3.16 49.41 95 0.15 11 6.8 35030 63.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.16 3.36 76.1 0.54 2.73 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2OH2 3.16 49.41 35013 1751 95 0.241 0.241 0.2341 0.278 0.2769 RANDOM 96.7
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] 33.42 -41.41 7.98
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.7 c_scangle_it 2.92 c_mcangle_it 2.21 c_improper_angle_d 1.77 c_scbond_it 1.7 c_angle_deg 1.4 c_mcbond_it 1.24 c_bond_d 0.008 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.7 c_scangle_it 2.92 c_mcangle_it 2.21 c_improper_angle_d 1.77 c_scbond_it 1.7 c_angle_deg 1.4 c_mcbond_it 1.24 c_bond_d 0.008 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6904 Nucleic Acid Atoms 1136 Solvent Atoms 30 Heterogen Atoms 66
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing