☰ Navigation Tabs
Crystal structure of HI0827, a hexameric broad specificity acyl-coenzyme A thioesterase: The Asp44Ala mutant enzyme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YLI PDB entry 1YLI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 Reservoir: 30% Saturated sodium citrate, 100 mM Hepes pH 7.5, 5% Ethylene glycol. Protein solution: 16 mg/mL protein in 10 mM Hepes pH 7.5, 150 mM KCl. Hanging drops: 1:1 reservoir and protein solutions. Cryoprotection: increasing ethylene glycol concentration to 18% under perfluoropolyether oil coat, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.56 51.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.487 α = 90 b = 63.108 β = 100.14 c = 104.718 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 IMAGE PLATE RIGAKU RAXIS IV++ Osmic mirrors 2003-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.9 30 98 0.065 8.2 6.1 79693 79693
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 PDB entry 1YLI 1.9 29.88 78077 78077 6353 99.94 0.172 0.172 0.169 0.21 0.2498 RANDOM 31.365
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] -0.12 -0.57 0.78 -0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.139 r_dihedral_angle_4_deg 16.755 r_dihedral_angle_3_deg 15.746 r_dihedral_angle_1_deg 6.183 r_scangle_it 3.697 r_scbond_it 2.424 r_angle_refined_deg 1.662 r_mcangle_it 1.54 r_mcbond_it 1.106 r_angle_other_deg 0.839
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.139 r_dihedral_angle_4_deg 16.755 r_dihedral_angle_3_deg 15.746 r_dihedral_angle_1_deg 6.183 r_scangle_it 3.697 r_scbond_it 2.424 r_angle_refined_deg 1.662 r_mcangle_it 1.54 r_mcbond_it 1.106 r_angle_other_deg 0.839 r_mcbond_other 0.273 r_symmetry_vdw_other 0.242 r_symmetry_vdw_refined 0.221 r_xyhbond_nbd_refined 0.198 r_nbd_refined 0.197 r_nbd_other 0.184 r_symmetry_hbond_refined 0.169 r_nbtor_refined 0.165 r_chiral_restr 0.097 r_nbtor_other 0.085 r_bond_refined_d 0.019 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6366 Nucleic Acid Atoms Solvent Atoms 463 Heterogen Atoms 139
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection CrystalClear data reduction CrystalClear data scaling CNS phasing