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Crystal structure of DNA N6-Adenine Methyltransferase M.BceJIV from Burkholderia cenocepacia in complex with duplex DNA substrates
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold experimental model PDB 6PBD To model the DNA molecules, the PDB entry 6PBD was utilized as a reference
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 50.38
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 2022-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.979338 NSLS-II 17-ID-2
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 2.11 97.39 94.6 0.101 0.998 9.2 4.7 49313
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 2.11 2.38 85 0.952 0.567 1.7
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.11 44.27 1.35 49285 2484 55.24 0.1864 0.1839 0.2342 0.2276
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 25.953 f_angle_d 0.841 f_chiral_restr 0.047 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7932 Nucleic Acid Atoms 2269 Solvent Atoms 551 Heterogen Atoms 61
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing