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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 4E1L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 295 0.2 M Ammonium fluride
20% (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.46 49.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 190.93 α = 90 b = 75.31 β = 131.42 c = 147.41 γ = 90
Symmetry Space Group C 1 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 IMAGE PLATE MAR scanner 345 mm plate 2014-10-13 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 1.8 35.6 99 0.14 4.3 4.6 135774
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 4E1L 1.8 35.6 129093 6673 99.4 0.162 0.16032 0.1717 0.19537 0.2057 RANDOM 28.293
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] 1.13 0.25 -1.02 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.142 r_dihedral_angle_4_deg 19.344 r_dihedral_angle_3_deg 12.082 r_dihedral_angle_1_deg 6.013 r_long_range_B_refined 4.784 r_long_range_B_other 4.784 r_scangle_other 3.103 r_scbond_it 2.2 r_scbond_other 2.2 r_mcangle_other 1.842
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.142 r_dihedral_angle_4_deg 19.344 r_dihedral_angle_3_deg 12.082 r_dihedral_angle_1_deg 6.013 r_long_range_B_refined 4.784 r_long_range_B_other 4.784 r_scangle_other 3.103 r_scbond_it 2.2 r_scbond_other 2.2 r_mcangle_other 1.842 r_mcangle_it 1.841 r_angle_refined_deg 1.802 r_angle_other_deg 1.538 r_mcbond_it 1.374 r_mcbond_other 1.369 r_chiral_restr 0.138 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_bond_other_d 0.01 r_gen_planes_other 0.007 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 11088 Nucleic Acid Atoms Solvent Atoms 1136 Heterogen Atoms 175
Software Software Software Name Purpose REFMAC refinement SCALA data reduction SCALA data scaling PHASER phasing