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Crystal Structure of Acyl-CoA transferase from E. coli O157:H7 (YdiF)-thioester complex with CoA- 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AHU PDB Entry 2AHU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7.5 293 16% (w/v) PEG 3350, 80 mM Na K tartarate, pH 7.5, Microbatch, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.43 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.085 α = 90 b = 140.24 β = 108.22 c = 112.682 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 315 2005-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.1 NSLS X29A
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 2 50 98.8 0.079 9 3.6 159093 159093 25.8
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 2 2.07 90.5 0.454 2 2.7 14536
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 PDB Entry 2AHU 2 50 156370 142009 14361 97.24 0.207 0.1862 0.18232 0.1836 0.22437 0.2255 RANDOM 25.933
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] 1.17 0.93 -1.3 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.997 r_dihedral_angle_3_deg 13.114 r_dihedral_angle_4_deg 12.876 r_dihedral_angle_1_deg 5.752 r_scangle_it 2.372 r_scbond_it 1.476 r_angle_refined_deg 1.183 r_mcangle_it 0.957 r_mcbond_it 0.576 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.997 r_dihedral_angle_3_deg 13.114 r_dihedral_angle_4_deg 12.876 r_dihedral_angle_1_deg 5.752 r_scangle_it 2.372 r_scbond_it 1.476 r_angle_refined_deg 1.183 r_mcangle_it 0.957 r_mcbond_it 0.576 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.224 r_nbd_refined 0.187 r_symmetry_hbond_refined 0.136 r_xyhbond_nbd_refined 0.126 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15618 Nucleic Acid Atoms Solvent Atoms 1474 Heterogen Atoms 192
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing