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Crystal structure of an N-acetyltransferase from Helicobacter pullorum in the presence of Coenzyme A and dTDP-3-acetamido-3,6-dideoxy-D-glucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7S3U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 15% PEG-5000, 5 mM dTDP-3-amino-3,6-dideoxy-D-glucose, 5 mM coenzyme A, 100 mM HEPES. Crystals were harvested and soaked in 20% PEG-5000, 200 mM NaCl, 5 mM dTDP-3-amino-3,6-dideoxy-D-glucose, 5 mM acetyl coenzyme A, 100 mM HEPES
Crystal Properties Matthews coefficient Solvent content 2.41 48.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.965 α = 90 b = 102.965 β = 90 c = 102.965 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 Bruker PHOTON II 2020-09-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.4 50 100 0.041 4.5 17.1 35803
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.5 99.9 0.234 4.5 11.7
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 7s3u 1.4 36.43 34048 1755 99.97 0.1638 0.1628 0.1726 0.1826 0.1921 RANDOM 12.433
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 r_dihedral_angle_4_deg 25.917 r_dihedral_angle_2_deg 25.889 r_dihedral_angle_3_deg 12.744 r_dihedral_angle_1_deg 8.062 r_angle_refined_deg 1.687 r_angle_other_deg 1.376 r_chiral_restr 0.38 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 25.917 r_dihedral_angle_2_deg 25.889 r_dihedral_angle_3_deg 12.744 r_dihedral_angle_1_deg 8.062 r_angle_refined_deg 1.687 r_angle_other_deg 1.376 r_chiral_restr 0.38 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.006 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1155 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction SAINT data reduction SADABS data scaling REFMAC phasing