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crystal structure of the 3-N-acetyl transferase WlbB from Bordetella petrii in complex with CoA and UDP-3-amino-2-acetamido-2,3-dideoxy glucuronic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MQG PDB ENTRY 3MQG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 295 16-20% PEG3400, 210 mM tetramethylammonium chloride, 100 mM HEPPS, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.64 53.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.466 α = 90 b = 107.891 β = 102.55 c = 91.269 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 210r 2009-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97921 APS 19-BM
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 1.43 50 90 0.077 0.077 28.3 2.9 213775 213775
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) 1.43 1.48 76.1 0.125 0.125 6.6 2.1 17966
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 (All) 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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 3MQG 1.43 30 213775 203089 10686 89.9 0.176 0.17578 0.17417 0.1664 0.20645 0.1959 RANDOM 13.093
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] -0.36 0.52 -0.74 1.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.894 r_dihedral_angle_4_deg 19.436 r_dihedral_angle_3_deg 12.373 r_dihedral_angle_1_deg 6.547 r_scangle_it 4.989 r_scbond_it 3.222 r_angle_refined_deg 2.124 r_mcangle_it 1.975 r_mcbond_it 1.291 r_chiral_restr 0.145
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.894 r_dihedral_angle_4_deg 19.436 r_dihedral_angle_3_deg 12.373 r_dihedral_angle_1_deg 6.547 r_scangle_it 4.989 r_scbond_it 3.222 r_angle_refined_deg 2.124 r_mcangle_it 1.975 r_mcbond_it 1.291 r_chiral_restr 0.145 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8690 Nucleic Acid Atoms Solvent Atoms 1698 Heterogen Atoms 612
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling