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8oxoguanine at the pre-insertion site of the polymerase active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L3S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.9 290 Ammonium sulfate, magnesium sulfate, mpd, mes, pH 5.90, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 3.2 61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.281 α = 90 b = 93.141 β = 90 c = 106.02 γ = 90
Symmetry Space Group P 21 21 21
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 double mirror optics 2003-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 2 41.09 92.1 0.05 20.3 8.5 59226 58360 -3 15.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.07 81.6 0.122 6.4 4503
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1L3S 2.01 41.09 59226 55802 2817 95.9 0.1941 0.1941 0.194 0.1965 0.227 0.2301 RANDOM 24.1
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] 2.94 -1.54 -1.4
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.3 c_scangle_it 1.34 c_angle_deg 1.2 c_mcangle_it 0.95 c_improper_angle_d 0.89 c_scbond_it 0.82 c_mcbond_it 0.55 c_bond_d 0.005 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.3 c_scangle_it 1.34 c_angle_deg 1.2 c_mcangle_it 0.95 c_improper_angle_d 0.89 c_scbond_it 0.82 c_mcbond_it 0.55 c_bond_d 0.005 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 4650 Nucleic Acid Atoms 406 Solvent Atoms 568 Heterogen Atoms 39
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling CNS refinement HKL-2000 data reduction CNS phasing