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Crystal Structure of Chloroflexus aurantiacus malyl-CoA lyase in complex with magnesium, oxalate, and propionyl-CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4L7Z PDB ENTRY 4L7Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 295 1 part protein solution (7.5 mg/mL in 20 mM Tris-HCl, pH 7.5, 2 mM magnesium chloride, 100 mM sodium chloride) + 2 parts buffer (0.1 M sodium cacodylate, pH 5.5, 20% w/v PEG4000) + 1 part substrate solution (20 mM Tris-HCl, pH 7.5, 2 mM magnesium chloride, 100 mM sodium chloride, 20 mM propionyl-CoA, 25 mM sodium oxalate, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.31 46.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.151 α = 90 b = 102.151 β = 90 c = 204.168 γ = 90
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 315r 2012-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.977408 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.008 37.93 99.8 0.106 15.1 5.1 138647 138647
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 2.008 2.12 99.2 0.637 0.637 1.2 5.1 20127
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 4L7Z 2.008 37.93 1.18 138596 1983 99.11 0.1729 0.1725 0.1726 0.201 0.201 28.2585
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.731 f_angle_d 0.907 f_chiral_restr 0.059 f_bond_d 0.006 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16114 Nucleic Acid Atoms Solvent Atoms 1689 Heterogen Atoms 370
Software Software Software Name Purpose SCALA data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction XDS data reduction