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Crystal structure of the adenine-specific DNA methyltransferase M.TaqI complexed with the cofactor analog AETA and a 10 bp DNA containing an abasic site analog at the target position
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G38 PDB ENTRY 1G38
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 298 3 microliters crystallization buffer (10 mM Tris/HCl, 300 mM NaCl, pH 7.3) containing the complex plus 1 microliter reservoir solution (100 mM KCl, 100 mM MgCl2, 6% isopropanol, 50 mM sodium cacodylate, pH 6.0), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.14 42.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.342 α = 90 b = 68.817 β = 92.22 c = 114.196 γ = 90
Symmetry Space Group P 1 21 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 CCD ADSC QUANTUM 4 ID14-3 (mirror) 2005-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.1 19.76 99 0.165 0.165 7.66 3.7 53925 53381 18.86
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.2 99.8 0.447 0.447 3.09 3.77 7006
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1G38 2.1 19.76 53850 53379 2668 99.13 0.23119 0.2283 0.2265 0.28624 0.2826 RANDOM 10.965
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] -0.57 0.2 0.13 0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.235 r_dihedral_angle_4_deg 16.61 r_dihedral_angle_3_deg 16.146 r_dihedral_angle_1_deg 6.291 r_scangle_it 1.545 r_angle_refined_deg 1.34 r_scbond_it 0.983 r_mcangle_it 0.712 r_mcbond_it 0.409 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.235 r_dihedral_angle_4_deg 16.61 r_dihedral_angle_3_deg 16.146 r_dihedral_angle_1_deg 6.291 r_scangle_it 1.545 r_angle_refined_deg 1.34 r_scbond_it 0.983 r_mcangle_it 0.712 r_mcbond_it 0.409 r_nbtor_refined 0.306 r_nbd_refined 0.188 r_symmetry_vdw_refined 0.156 r_symmetry_hbond_refined 0.149 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6389 Nucleic Acid Atoms 790 Solvent Atoms 526 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement ProDC data collection MAR345 data collection XDS data scaling MOLREP phasing