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crystal structure of the 3-N-acetyl transferase WlbB from Bordetella petrii in complex with acetyl-CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other In house low resolution model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 295 15-20% PEG3400, 210 mM tetramethyl ammonium chloride, 100 mM HEPPS, 10 mM UDP, 10 mM acetyl-CoA, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.63 53.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.488 α = 90 b = 107.824 β = 102.49 c = 90.966 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 2009-11-13 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 95.6 0.07 0.07 38.2 3.9 226783 226783
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 88.7 0.141 0.141 8.9 2.7 20999
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT In house low resolution model 1.43 30 226763 215388 11375 95.6 0.192 0.19183 0.19049 0.21714 0.2154 RANDOM 14.361
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] -0.39 0.3 -0.74 1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.553 r_dihedral_angle_4_deg 18.125 r_dihedral_angle_3_deg 13.374 r_dihedral_angle_1_deg 6.539 r_scangle_it 5.608 r_scbond_it 3.661 r_mcangle_it 2.203 r_angle_refined_deg 2.18 r_mcbond_it 1.397 r_chiral_restr 0.146
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.553 r_dihedral_angle_4_deg 18.125 r_dihedral_angle_3_deg 13.374 r_dihedral_angle_1_deg 6.539 r_scangle_it 5.608 r_scbond_it 3.661 r_mcangle_it 2.203 r_angle_refined_deg 2.18 r_mcbond_it 1.397 r_chiral_restr 0.146 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 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 8675 Nucleic Acid Atoms Solvent Atoms 1449 Heterogen Atoms 496
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling