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Dpo4 post-extension ternary complex with the correct C opposite the 2-aminofluorene-guanine [AF]G lesion
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 VAPOR DIFFUSION, HANGING DROP 7 293 100 mM HEPES pH 7.0, 100 mM Calcium acetate, 10% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.59 52.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.477 α = 81.76 b = 53.019 β = 76.76 c = 99.858 γ = 70.14
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 2007-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97914 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 20 96.7 0.075 15.9 4 63173 2
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 2.05 96.3 0.469 3.3 4 4779
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 2.01 20 59976 3185 95.9 0.20822 0.20619 0.2145 0.2465 0.2544 RANDOM 33.588
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] 0.4 0.81 -0.54 -1.31 1.28 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.852 r_dihedral_angle_4_deg 17.692 r_dihedral_angle_3_deg 15.979 r_dihedral_angle_1_deg 4.913 r_scangle_it 2.821 r_scbond_it 1.743 r_angle_refined_deg 1.444 r_mcangle_it 1.296 r_mcbond_it 0.802 r_chiral_restr 0.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.852 r_dihedral_angle_4_deg 17.692 r_dihedral_angle_3_deg 15.979 r_dihedral_angle_1_deg 4.913 r_scangle_it 2.821 r_scbond_it 1.743 r_angle_refined_deg 1.444 r_mcangle_it 1.296 r_mcbond_it 0.802 r_chiral_restr 0.101 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5480 Nucleic Acid Atoms 1233 Solvent Atoms 402 Heterogen Atoms 92
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling