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Dpo4 extension ternary complex with 3'-terminal primer G base opposite the 1-methylguanine (M1G) lesion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RAQ PDB ENTRY 3RAQ
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 2.96 58.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.421 α = 90 b = 110.362 β = 101.28 c = 102.268 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 100 CCD ADSC QUANTUM 315 2006-12-17 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) 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 3.2 20 96.6 3.4 18330 17707 2 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 3.2 3.31 83.7 2 1.9
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 3RAQ 3.225 20 2 17707 16783 893 95.81 0.22719 0.2234 0.2293 0.29409 0.3098 RANDOM 108.231
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] -3.08 2.64 -1.79 5.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.906 r_dihedral_angle_3_deg 19.291 r_dihedral_angle_4_deg 14.535 r_dihedral_angle_1_deg 6.754 r_scangle_it 2.366 r_angle_refined_deg 1.441 r_scbond_it 1.184 r_angle_other_deg 0.84 r_mcangle_it 0.58 r_mcbond_it 0.363
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.906 r_dihedral_angle_3_deg 19.291 r_dihedral_angle_4_deg 14.535 r_dihedral_angle_1_deg 6.754 r_scangle_it 2.366 r_angle_refined_deg 1.441 r_scbond_it 1.184 r_angle_other_deg 0.84 r_mcangle_it 0.58 r_mcbond_it 0.363 r_chiral_restr 0.097 r_mcbond_other 0.032 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5479 Nucleic Acid Atoms 1181 Solvent Atoms 31 Heterogen Atoms 68
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling