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Crystal structure of peroxisomal citrate synthase (Cit2) from Saccharomyces cerevisiae in complex with oxaloacetate and coenzyme-A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 80 mM KCl, 80 mM HEPES pH 7.5, 12% (w/v) PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.42 49.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.079 α = 90 b = 129.659 β = 116.574 c = 68.127 γ = 90
Symmetry Space Group P 1 21 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 RAYONIX MX300HE 2016-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.900 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.48 34.13 99.09 0.998 23.68 4.3 160915 17.45
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.48 1.53 0.838 4.02
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FREE R-VALUE 1.48 34.13 1.34 160885 3979 98.52 0.1782 0.178 0.1779 0.1978 0.197 24.39
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 11.3627 f_angle_d 0.7014 f_chiral_restr 0.0664 f_plane_restr 0.004 f_bond_d 0.0036
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6868 Nucleic Acid Atoms Solvent Atoms 819 Heterogen Atoms 81
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHASER phasing PHENIX refinement