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Structural basis for thymine glycosylase activity on T:O6-methylG mismatch by methyl-CpG binding domain protein 4: Implications for roles of Arg468 in mismatch recognition and catalysis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4E9G PDB ENTRY 4E9G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 295 15% PEG1500, 0.1M MES at pH of 6.5, 0.2M Na Acetate., VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.03 39.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.722 α = 90 b = 55.605 β = 90 c = 104.245 γ = 90
Symmetry Space Group P 21 21 21
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 315r 2013-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.97648 ALS 5.0.3
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 2.15 50 99.7 13802
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 4E9G 2.15 33.39 12344 647 94.12 0.14506 0.14223 0.1496 0.20153 0.202 RANDOM 28.328
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] 0.16 0.06 -0.22
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 33.636 r_dihedral_angle_2_deg 30.807 r_sphericity_bonded 19.656 r_dihedral_angle_4_deg 15.794 r_dihedral_angle_3_deg 13.906 r_rigid_bond_restr 7.166 r_dihedral_angle_1_deg 5.285 r_angle_other_deg 1.38 r_angle_refined_deg 1.237 r_chiral_restr 0.075
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 33.636 r_dihedral_angle_2_deg 30.807 r_sphericity_bonded 19.656 r_dihedral_angle_4_deg 15.794 r_dihedral_angle_3_deg 13.906 r_rigid_bond_restr 7.166 r_dihedral_angle_1_deg 5.285 r_angle_other_deg 1.38 r_angle_refined_deg 1.237 r_chiral_restr 0.075 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1208 Nucleic Acid Atoms 487 Solvent Atoms 133 Heterogen Atoms 1
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling