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Crystal structure of Arthrobacter sp. strain SU 4-hydroxybenzoyl CoA thioesterase mutant Q58A complexed with 4-hydroxybenzoic acid and CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Q4S PSB entry 1Q4S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 20% PEG3400, 100 mM MOPS, 200 mM LiCl, 1 mM 4-Hydroxybenzoyl-CoA, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.36 63.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.6 α = 90 b = 112.6 β = 90 c = 60 γ = 120
Symmetry Space Group P 32 2 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 AREA DETECTOR SIEMENS HI-STAR goebel mirrors 2002-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.54178
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 1.8 100 95.2 0.059 0.059 35.1 4.8 36932 36932
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 1.8 1.85 83.3 0.261 0.261 2.2 2.1 2340
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 PSB entry 1Q4S 1.8 97.51 36932 36932 1960 95.15 0.18552 0.18552 0.18407 0.1775 0.212 0.2047 RANDOM 28.381
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] -1.15 -0.57 -1.15 1.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.042 r_dihedral_angle_4_deg 15.645 r_dihedral_angle_3_deg 13.878 r_dihedral_angle_1_deg 6.455 r_scangle_it 5.792 r_scbond_it 4.155 r_mcangle_it 2.576 r_angle_refined_deg 2.176 r_mcbond_it 1.77 r_chiral_restr 0.157
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.042 r_dihedral_angle_4_deg 15.645 r_dihedral_angle_3_deg 13.878 r_dihedral_angle_1_deg 6.455 r_scangle_it 5.792 r_scbond_it 4.155 r_mcangle_it 2.576 r_angle_refined_deg 2.176 r_mcbond_it 1.77 r_chiral_restr 0.157 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2135 Nucleic Acid Atoms Solvent Atoms 269 Heterogen Atoms 116
Software Software Software Name Purpose FRAMBO data collection AMoRE phasing REFMAC refinement SAINT data reduction SAINT data scaling