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Structure of human DNA polymerase beta complexed with O6MG as the template base in a 1-nucleotide gapped DNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 14% 23% PEG3400, and 350 mM sodium acetate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.44 49.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.438 α = 90 b = 79.265 β = 105.66 c = 54.789 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2013-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 20 95.7 16418 16418 1 1
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 MOLECULAR REPLACEMENT THROUGHOUT 2.4 19.816 15979 799 90.6 0.2022 0.1981 0.198 0.2791 0.2771 RANDOM 32.7525
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] 1.77 1.58 -0.7 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.971 r_dihedral_angle_3_deg 17.438 r_dihedral_angle_4_deg 15.518 r_dihedral_angle_1_deg 5.912 r_angle_refined_deg 1.62 r_chiral_restr 0.094 r_bond_refined_d 0.011 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2558 Nucleic Acid Atoms 633 Solvent Atoms 53 Heterogen Atoms 2
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection MOLREP phasing