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Ternary complex of Dpo4 bound to N2,N2-dimethyl-deoxyguanosine modified DNA with incoming dGTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JEF PDB ENTRY 2JEF
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, 1 MM DGTP.
Crystal Properties Matthews coefficient Solvent content 2.44 53.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.67 α = 90 b = 103.757 β = 90 c = 52.75 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 2008-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID APS 21-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 2.55 19.94 98.2 0.06 23.3 6.8 16285 42.4
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 2.55 2.69 97.4 0.2 5.3 6.2
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 2JEF 2.6 19.94 16285 790 98.3 0.213 0.213 0.2127 0.246 0.2387 RANDOM 42.7
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] 5.69 -3.13 -2.56
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.9 c_scangle_it 2.95 c_mcangle_it 2.12 c_scbond_it 1.85 c_improper_angle_d 1.83 c_angle_deg 1.4 c_mcbond_it 1.23 c_bond_d 0.009 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.9 c_scangle_it 2.95 c_mcangle_it 2.12 c_scbond_it 1.85 c_improper_angle_d 1.83 c_angle_deg 1.4 c_mcbond_it 1.23 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 609 Solvent Atoms 65 Heterogen Atoms 35
Software Software Software Name Purpose CNS refinement XDS data reduction XDS data scaling MOLREP phasing