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Crystal structure of Thiolase from Pseudomonas aeruginosa PAO1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WYR 4wyr
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 35% (v/v) 2-Ethoxyethanol
100 mM Sodium citrate/citric acid, pH 5.5
Crystal Properties Matthews coefficient Solvent content 4.26 71.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.565 α = 90 b = 146.565 β = 90 c = 122.876 γ = 120
Symmetry Space Group P 31 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 CCD ADSC QUANTUM 270 2019-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.9793 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 97.2 0.118 0.126 0.045 12.3 6 80669
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.19 95.9 0.294 0.326 0.136 0.918 4.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 4wyr 2.15 31.49 76571 4088 97.13 0.1673 0.1656 0.1757 0.1993 0.2049 RANDOM 40.374
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] 1.23 0.62 1.23 -4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.09 r_dihedral_angle_4_deg 17.808 r_dihedral_angle_3_deg 14.176 r_dihedral_angle_1_deg 7.268 r_angle_refined_deg 1.808 r_angle_other_deg 1.459 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.09 r_dihedral_angle_4_deg 17.808 r_dihedral_angle_3_deg 14.176 r_dihedral_angle_1_deg 7.268 r_angle_refined_deg 1.808 r_angle_other_deg 1.459 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5716 Nucleic Acid Atoms Solvent Atoms 358 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing