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Non-productive complex of the Y-family DNA polymerase Dpo4 with dGTP skipping the M1dG adduct to pair with the next template cytosine
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 VAPOR DIFFUSION, SITTING DROP 7.4 7.5% POLYETHYLENE GLYCOL 3350, 100 MM CALCIUM ACETATE, 25 MM TRIS HCL (PH 7.4), 100 MM SODIUM CHLORIDE, 2.5% GLYCEROL, 1 MM DGTP, 5 MM CALCIUM CHLORIDE.
Crystal Properties Matthews coefficient Solvent content 3.1 59.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.545 α = 90 b = 102.537 β = 90 c = 52.176 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 2008-04-12 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 2.5 30 97.5 0.087 10.89 3.7 17552 47.1
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 2.5 2.59 99.5 0.344 3.9 4
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 2.5 29.83 17552 848 97.7 0.218 0.218 0.2172 0.273 0.2782 RANDOM 44.6
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] 9.72 -6.54 -3.18
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.7 c_scangle_it 3.14 c_improper_angle_d 2.48 c_mcangle_it 2.32 c_scbond_it 1.98 c_mcbond_it 1.35 c_angle_deg 1.3 c_bond_d 0.008 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.7 c_scangle_it 3.14 c_improper_angle_d 2.48 c_mcangle_it 2.32 c_scbond_it 1.98 c_mcbond_it 1.35 c_angle_deg 1.3 c_bond_d 0.008 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 611 Solvent Atoms 134 Heterogen Atoms 34
Software Software Software Name Purpose CNS refinement XDS data reduction SCALEPACK data scaling MOLREP phasing