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Crystal structure of FdtD, a bifunctional ketoisomerase/N-acetyltransferase from Shewanella denitrificans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other model from SAD experiment
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 100 mM HEPPS, 7-12% PEG-8000, 100 mM MgCl2, 10 mM dTDP, 10 mM CoA, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.76 55.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.314 α = 79.23 b = 109.443 β = 79.98 c = 127.847 γ = 84.89
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 mirrors 2012-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9794 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 2.2 30 91.1 0.071 0.071 27 3 205722 205772
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 2.2 2.28 87 0.223 0.223 4.7 2.5 19668
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 MOLECULAR REPLACEMENT THROUGHOUT model from SAD experiment 2.2 30 205772 195488 10284 90.88 0.20751 0.20751 0.20421 0.2043 0.26985 0.2681 RANDOM 35.626
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] 0.45 1.16 0.58 -2.13 0.57 1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.011 r_dihedral_angle_4_deg 23.834 r_dihedral_angle_3_deg 19.948 r_dihedral_angle_1_deg 7.804 r_scangle_it 5.063 r_scbond_it 3.287 r_angle_refined_deg 2.23 r_mcangle_it 2.051 r_mcbond_it 1.133 r_chiral_restr 0.153
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.011 r_dihedral_angle_4_deg 23.834 r_dihedral_angle_3_deg 19.948 r_dihedral_angle_1_deg 7.804 r_scangle_it 5.063 r_scbond_it 3.287 r_angle_refined_deg 2.23 r_mcangle_it 2.051 r_mcbond_it 1.133 r_chiral_restr 0.153 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 26574 Nucleic Acid Atoms Solvent Atoms 847 Heterogen Atoms 962
Software Software Software Name Purpose HKL-3000 data collection SOLVE phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling