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Structure of the enzyme-product complex resulting from TDG action on a GfC mismatch
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 2.66 48.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.15 α = 90 b = 53.82 β = 95.55 c = 81.15 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 2014-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.979 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 2.02 38.95 99.7 11 18 26946 39.56
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 2.02 2.32 96.8 0.068 0.3 15.5
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 2.02 32.45 26944 1206 98.68 0.1891 0.1871 0.2 0.2325 0.2418 RANDOM 57.23
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] -10.6404 6.8993 3.1058 7.5346
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 21.83 t_omega_torsion 3.4 t_angle_deg 1.01 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 21.83 t_omega_torsion 3.4 t_angle_deg 1.01 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 1530 Nucleic Acid Atoms 1135 Solvent Atoms 143 Heterogen Atoms 12
Software Software Software Name Purpose BUSTER refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction Blu-Ice data collection XDS data reduction