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Crystal structure of Arthrobacter sp. strain SU 4-hydroxybenzoyl CoA thioesterase mutant Q58A complexed with 4-hydroxyphenacyl CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Q4S PDB 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, 1mM 4-HYDROXYPHENACYL COA, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.32 62.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.5 α = 90 b = 112.5 β = 90 c = 59.5 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 2002-05-23 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 94.2 0.058 0.058 34.9 4.6 36193 36193
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 0.251 0.251 3.1 2.1 2347
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 1Q4S 1.8 97.43 36193 36193 1899 94.18 0.18457 0.18457 0.18265 0.1772 0.22119 0.2155 RANDOM 28.176
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] -0.45 -0.22 -0.45 0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.313 r_dihedral_angle_4_deg 14.741 r_dihedral_angle_3_deg 13.432 r_dihedral_angle_1_deg 5.851 r_scangle_it 5.445 r_scbond_it 3.797 r_mcangle_it 2.415 r_angle_refined_deg 2.034 r_mcbond_it 1.522 r_chiral_restr 0.154
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.313 r_dihedral_angle_4_deg 14.741 r_dihedral_angle_3_deg 13.432 r_dihedral_angle_1_deg 5.851 r_scangle_it 5.445 r_scbond_it 3.797 r_mcangle_it 2.415 r_angle_refined_deg 2.034 r_mcbond_it 1.522 r_chiral_restr 0.154 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 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 258 Heterogen Atoms 116
Software Software Software Name Purpose FRAMBO data collection AMoRE phasing REFMAC refinement SAINT data reduction SAINT data scaling