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X-ray crystal structure of a thiolase from Escherichia coli at 1.8 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5F0V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 295 0.1 M Bis-tris propane pH 8.0, 35% PEG6000, 0.05 LiCl2
Crystal Properties Matthews coefficient Solvent content 2.34 47.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.794 α = 90 b = 76.254 β = 90 c = 266.607 γ = 90
Symmetry Space Group P 21 21 21
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 MAR scanner 345 mm plate 2014-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
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 36.8 99.5 0.0117 2.1 12.6 150897
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 99.5 0.117 2.1 12.6
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 5F0V 1.9 36.8 113201 5910 99.71 0.19865 0.19673 0.2035 0.23481 0.2399 RANDOM 29.74
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] -0.95 1.04 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.629 r_dihedral_angle_4_deg 18.861 r_dihedral_angle_3_deg 11.936 r_long_range_B_refined 6.852 r_long_range_B_other 6.741 r_dihedral_angle_1_deg 5.893 r_scangle_other 1.9 r_angle_refined_deg 1.733 r_scbond_it 1.347 r_scbond_other 1.347
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.629 r_dihedral_angle_4_deg 18.861 r_dihedral_angle_3_deg 11.936 r_long_range_B_refined 6.852 r_long_range_B_other 6.741 r_dihedral_angle_1_deg 5.893 r_scangle_other 1.9 r_angle_refined_deg 1.733 r_scbond_it 1.347 r_scbond_other 1.347 r_angle_other_deg 1.326 r_mcangle_it 1.149 r_mcangle_other 1.149 r_mcbond_it 0.732 r_mcbond_other 0.73 r_chiral_restr 0.111 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d 0.009 r_gen_planes_other 0.006 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10760 Nucleic Acid Atoms Solvent Atoms 1033 Heterogen Atoms 172
Software Software Software Name Purpose REFMAC refinement SCALA data reduction SCALA data scaling PHASER phasing