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Structure of the enzyme-product complex resulting from TDG action on a GU 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 2.44 49.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.305 α = 90 b = 53.322 β = 95.31 c = 82.297 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 PSI PILATUS 6M 2014-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 1.00000 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 1.45 45.73 94.9 0.068 0.02 0.999 15.9 11.7 64847 27.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.47 89.8 0.722 0.645 1.2 11 2991
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 1.45 45.73 61716 3110 94.75 0.1428 0.1403 0.1488 0.1953 0.1997 RANDOM 37.444
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] 1.6 -0.65 -0.28 -1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.638 r_sphericity_free 29.915 r_sphericity_bonded 18.998 r_dihedral_angle_4_deg 17.134 r_dihedral_angle_3_deg 13.329 r_dihedral_angle_1_deg 6.665 r_mcangle_it 6.399 r_rigid_bond_restr 5.985 r_mcbond_it 4.961 r_mcbond_other 4.938
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.638 r_sphericity_free 29.915 r_sphericity_bonded 18.998 r_dihedral_angle_4_deg 17.134 r_dihedral_angle_3_deg 13.329 r_dihedral_angle_1_deg 6.665 r_mcangle_it 6.399 r_rigid_bond_restr 5.985 r_mcbond_it 4.961 r_mcbond_other 4.938 r_angle_refined_deg 2.274 r_angle_other_deg 1.919 r_chiral_restr 0.151 r_bond_refined_d 0.023 r_gen_planes_refined 0.019 r_gen_planes_other 0.013 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1557 Nucleic Acid Atoms 1135 Solvent Atoms 277 Heterogen Atoms 16
Software Software Software Name Purpose MOSFLM data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection