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Crystal Structure of Acyl-CoA transferase from E. coli O157:H7 (YdiF)-thioester complex with CoA- 2
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 = 80.883 α = 90 b = 137.095 β = 105.83 c = 110.424 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 2.15 50 98.9 0.063 11.9 3.5 173535 124447
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 2.15 2.23 95.4 0.483 2.14 3
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 (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 2.15 50 124447 112953 11494 99.1 0.19055 0.18592 0.1861 0.23545 0.2357 RANDOM 35.817
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 0.63 -0.55 0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.617 r_dihedral_angle_3_deg 14.011 r_dihedral_angle_4_deg 13.841 r_dihedral_angle_1_deg 6.026 r_scangle_it 2.475 r_scbond_it 1.566 r_angle_refined_deg 1.239 r_mcangle_it 1.055 r_mcbond_it 0.624 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.617 r_dihedral_angle_3_deg 14.011 r_dihedral_angle_4_deg 13.841 r_dihedral_angle_1_deg 6.026 r_scangle_it 2.475 r_scbond_it 1.566 r_angle_refined_deg 1.239 r_mcangle_it 1.055 r_mcbond_it 0.624 r_nbtor_refined 0.305 r_nbd_refined 0.192 r_symmetry_vdw_refined 0.183 r_symmetry_hbond_refined 0.168 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 15370 Nucleic Acid Atoms Solvent Atoms 1304 Heterogen Atoms 144
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing