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Crystal structure of DNA N6-Adenine Methyltransferase M.BceJIV from Burkholderia cenocepacia in complex with duplex DNA substrate containing GTATAC as recognition sequence
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8URK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293.15 0.10% w/v n-Octyl-beta-D-glucoside, 0.1 M Sodium citrate tribasic dihydrate pH 5.5, and 22% w/v Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.48 50.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.728 α = 90 b = 137.728 β = 90 c = 167.315 γ = 90
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 EIGER X 16M 2024-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.979338 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.16 32.91 91.9 0.102 0.998 10.1 5.4 41892
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.17 2.52 0.887 0.627 1.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.16 32.76 1.36 41883 2090 50.59 0.1917 0.189 0.1999 0.2437 0.2445
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 25.835 f_angle_d 0.717 f_chiral_restr 0.043 f_plane_restr 0.006 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7563 Nucleic Acid Atoms 2269 Solvent Atoms 316 Heterogen Atoms 131
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing