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Structural Basis for Proficient Incorporation of dTTP Opposite O6-Methylguanine by Human DNA Polymerase Iota
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ALZ 2ALZ minus DNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 0.2 M Ammonium Sulfate, 12.5% PEG 5000 monomethylether, 0.1 M MES buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.42 49.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.973 α = 90 b = 97.973 β = 90 c = 202.757 γ = 120
Symmetry Space Group P 65 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD Mirrors and beryllium lenses 2010-08-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.00 APS 21-ID-D
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 1.9 47.62 99.8 0.068 37.9 15.7 46192
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) 1.9 1.97 98.9 0.525 3.2 8.8 4478
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 2ALZ minus DNA 1.9 47.62 43636 2327 99.5 0.2098 0.20814 0.2383 0.24127 0.2694 RANDOM 52.544
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] 0.59 0.29 0.59 -0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.184 r_dihedral_angle_4_deg 20.013 r_dihedral_angle_3_deg 17.759 r_dihedral_angle_1_deg 6.337 r_scangle_it 4.136 r_scbond_it 2.795 r_angle_refined_deg 2.284 r_mcangle_it 1.655 r_mcbond_it 0.979 r_chiral_restr 0.164
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.184 r_dihedral_angle_4_deg 20.013 r_dihedral_angle_3_deg 17.759 r_dihedral_angle_1_deg 6.337 r_scangle_it 4.136 r_scbond_it 2.795 r_angle_refined_deg 2.284 r_mcangle_it 1.655 r_mcbond_it 0.979 r_chiral_restr 0.164 r_bond_refined_d 0.026 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2999 Nucleic Acid Atoms 309 Solvent Atoms 271 Heterogen Atoms 32
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling