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Crystal structure of Acyl-CoA transferase (YdiF) apoenzyme from Escherichia coli O157:H7.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 294 22.5 % (w/v) PEG 4000, 3% (v/v) isopropanol and 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.43 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.129 α = 90 b = 133.308 β = 100.57 c = 105.838 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 4 mirrors 2004-06-12 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 4 mirrors 2004-06-12 M MAD 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X8C 1.1 NSLS X8C 2 SYNCHROTRON NSLS BEAMLINE X8C 0.9799, 0.9795, 0.9646 NSLS X8C
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 1.9 50 94.3 0.053 20.1 3 491266 163843
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 1.9 1.97 71.8 0.284 4.4 2.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.9 50 163804 148789 15015 94.34 0.19026 0.18714 0.1878 0.22044 0.2209 RANDOM 27.689
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] 0.78 0.27 -0.65 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.572 r_dihedral_angle_4_deg 15.175 r_dihedral_angle_3_deg 14.498 r_dihedral_angle_1_deg 5.321 r_scangle_it 2.759 r_scbond_it 1.808 r_angle_refined_deg 1.143 r_mcangle_it 1.048 r_mcbond_it 0.697 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.572 r_dihedral_angle_4_deg 15.175 r_dihedral_angle_3_deg 14.498 r_dihedral_angle_1_deg 5.321 r_scangle_it 2.759 r_scbond_it 1.808 r_angle_refined_deg 1.143 r_mcangle_it 1.048 r_mcbond_it 0.697 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.195 r_nbd_refined 0.184 r_symmetry_hbond_refined 0.136 r_xyhbond_nbd_refined 0.118 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 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 15696 Nucleic Acid Atoms Solvent Atoms 1271 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling SOLVE phasing