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Y-family DNA polymerase Dpo4 bypassing N2-naphthyl-guanine adduct in anti orientation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BQR PDB ENTRY 2BQR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.4 DPO4:DNA COMPLEX (1:1.2 MOLAR RATIO, 150 MICROMOLAR), 20 MM TRIS HCL (PH 7.4), 15% POLYETHYLENE GLYCOL 3350 (W/V), 60 MM SODIUM CHLORIDE, 5 MM MAGNESIUM CHLORIDE, 4% GLYCEROL, 1 MM DGTP.
Crystal Properties Matthews coefficient Solvent content 2.61 52.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.919 α = 90 b = 103.832 β = 90 c = 52.493 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 MIRRORS 2008-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID APS 22-ID
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 3 42.11 99.6 0.08 23.37 6.6 11751 57.3
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) 1 3 3.19 100 0.77 4.7 7.3
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 2BQR 3 29.25 10584 560 98.5 0.226 0.226 0.2232 0.282 0.2692 RANDOM 77.4
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] 5.56 -1.48 -4.09
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.2 c_scangle_it 3.5 c_mcangle_it 2.61 c_scbond_it 2.25 c_improper_angle_d 1.77 c_angle_deg 1.6 c_mcbond_it 1.5 c_bond_d 0.009 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.2 c_scangle_it 3.5 c_mcangle_it 2.61 c_scbond_it 2.25 c_improper_angle_d 1.77 c_angle_deg 1.6 c_mcbond_it 1.5 c_bond_d 0.009 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 2754 Nucleic Acid Atoms 618 Solvent Atoms 43 Heterogen Atoms 34
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing