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Crystal structures of mutant Dpo4 DNA polymerases with 8-oxoG containing DNA template-primer constructs
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2UVR PDB ENTRY 2UVR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 8% PEG 3350, 10 MM TRIS-HCL PH 7.5, 50 MM CA(CH3CO2)2, 50MM NACL, 3.5% GLYCEROL
Crystal Properties Matthews coefficient Solvent content 2.6 54.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.778 α = 90 b = 103.728 β = 90 c = 52.915 γ = 90
Symmetry Space Group P 21 21 2
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 2006-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 5ID-B APS 5ID-B
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 2.09 32.26 92.3 0.05 12.43 3.45 29759 1 46.6
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 2.09 2.17 70.2 0.44 1.5 2.8
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 2UVR 2.09 30.81 29750 1468 92.3 0.249 0.249 0.2322 0.274 0.2589 RANDOM 46.1
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] 1.54 -0.43 -1.11
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.3 c_scangle_it 2.95 c_mcangle_it 2.24 c_scbond_it 1.95 c_improper_angle_d 1.49 c_mcbond_it 1.38 c_angle_deg 1.3 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.3 c_scangle_it 2.95 c_mcangle_it 2.24 c_scbond_it 1.95 c_improper_angle_d 1.49 c_mcbond_it 1.38 c_angle_deg 1.3 c_bond_d 0.007 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 2742 Nucleic Acid Atoms 634 Solvent Atoms 224 Heterogen Atoms 34
Software Software Software Name Purpose CNS refinement X-GEN data reduction X-GEN data scaling CNS phasing