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Binary complex of Dpo4 bound to N2,N2-dimethyl-deoxyguanosine modified DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ASD PDB ENTRY 2ASD
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 2.42 53.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.794 α = 90 b = 101.776 β = 91.95 c = 97.268 γ = 90
Symmetry Space Group P 1 21 1
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 2008-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F APS 21-ID-F
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 2.28 28.75 96.4 0.1 10.3 3.9 45625 41
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 2.28 2.42 89.7 0.26 3.8 6.8
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 2ASD 2.28 28.75 44372 2231 96.4 0.239 0.239 0.2361 0.251 0.2488 RANDOM 36.3
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] 1.38 2.31 -5.52 4.14
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.5 c_scangle_it 3.64 c_angle_deg 3.2 c_scbond_it 2.75 c_improper_angle_d 2.39 c_mcangle_it 2.27 c_mcbond_it 1.4 c_bond_d 0.034 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.5 c_scangle_it 3.64 c_angle_deg 3.2 c_scbond_it 2.75 c_improper_angle_d 2.39 c_mcangle_it 2.27 c_mcbond_it 1.4 c_bond_d 0.034 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 5500 Nucleic Acid Atoms 1220 Solvent Atoms 203 Heterogen Atoms 4
Software Software Software Name Purpose CNS refinement XDS data reduction XDS data scaling MOLREP phasing