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Structure of the enzyme-product complex resulting from TDG action on a GT mismatch in the presence of excess base
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FNC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 298 30% PEG 4000, 0.2M ammonium acetate, 0.1M sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.48 50.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.729 α = 90 b = 53.46 β = 95.54 c = 82.033 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS PILATUS 6M 2014-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 1.00 SSRL BL12-2
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 1.83 39.26 98.5 10.2 8.8 34165 34.67
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 1.83 1.87 91.5 0.057 0.4 3
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 4FNC 1.83 39.26 34036 1660 98.1 0.195 0.193 0.2079 0.237 0.2521 RANDOM 55.85
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] -13.586 1.8657 2.0191 11.5669
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 21.74 t_omega_torsion 3.35 t_angle_deg 0.99 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 21.74 t_omega_torsion 3.35 t_angle_deg 0.99 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1535 Nucleic Acid Atoms 894 Solvent Atoms 205 Heterogen Atoms 249
Software Software Software Name Purpose BUSTER-TNT refinement Aimless data scaling PDB_EXTRACT data extraction Blu-Ice data collection PHASER phasing XDS data reduction