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Dpo4 extension ternary complex with 3'-terminal primer C base opposite the 1-methylguanine (MG1) lesion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GIJ PDB ENTRY 3GIJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 100 mM HEPES, pH 7.0, 100 mM calcium acetate and 10% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.89 57.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.194 α = 98.97 b = 62.077 β = 103.82 c = 91.459 γ = 93.72
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD ADSC QUANTUM 315 2006-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97949 APS 24-ID-C
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 2.25 20 98.4 0.107 3.6 51859 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.31 96.8 2 2.8 3622
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 3GIJ 2.25 20 2 51859 48438 2578 98.27 0.19589 0.19379 0.204 0.23505 0.2428 RANDOM 44.889
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] -2.05 0.06 -0.32 0.05 -0.05 1.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.672 r_dihedral_angle_4_deg 18.619 r_dihedral_angle_3_deg 14.87 r_dihedral_angle_1_deg 5.2 r_scangle_it 2.04 r_angle_refined_deg 1.42 r_scbond_it 1.259 r_angle_other_deg 0.895 r_mcangle_it 0.883 r_mcbond_it 0.523
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.672 r_dihedral_angle_4_deg 18.619 r_dihedral_angle_3_deg 14.87 r_dihedral_angle_1_deg 5.2 r_scangle_it 2.04 r_angle_refined_deg 1.42 r_scbond_it 1.259 r_angle_other_deg 0.895 r_mcangle_it 0.883 r_mcbond_it 0.523 r_chiral_restr 0.118 r_mcbond_other 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5480 Nucleic Acid Atoms 1237 Solvent Atoms 298 Heterogen Atoms 98
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling