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Human DNA Polymerase Beta Complexed With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine Template Paired with dCTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BPY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 291 14% PEG 3350, 350 mM sodium acetate and 50 mM imidazole at 18 degrees (C), pH 7.5, temperature 291.0K
Crystal Properties Matthews coefficient Solvent content 2.22 44.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.5 α = 90 b = 79.9 β = 107.9 c = 55.6 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 200 IMAGE PLATE RIGAKU RAXIS IV M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300
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 2.8 20 97.8 0.108 5.5 2.51 10209 -3
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) 2.8 2.93 95.9 0.339 1.9
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1BPY 2.8 20 10177 10177 481 97.8 0.246 0.246 0.235 0.295 RANDOM 22.42
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] -14.235 -15.806 18.549 -4.313
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 2.869 c_scbond_it 2.186 c_mcangle_it 1.855 c_mcbond_it 1.324 c_angle_deg 1.1 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2613 Nucleic Acid Atoms 632 Solvent Atoms 78 Heterogen Atoms 31
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement CNS phasing