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Glyoxysomal Citrate Synthase 3 from Arabidopsis thaliana in complex with OAA and CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4G6B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 20mM CoA and 20mM OAA in 90mM HEPES pH7.0, 9mM MgCl2, 18%(w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.01 38.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 193.859 α = 90 b = 60.597 β = 90 c = 76.864 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2019-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 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 1.7 38.32 98.6 0.999 17.1 6.7 100323
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 1.7 1.74 0.926
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.7 38.32 99058 1977 98.63 0.159 0.1659 0.172 0.1967 0.2059 29.84
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] -1.547 0.791 0.757
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.31 r_dihedral_angle_3_deg 12.989 r_lrange_it 7.531 r_lrange_other 7.531 r_dihedral_angle_1_deg 6.135 r_scangle_it 5.981 r_scangle_other 5.98 r_dihedral_angle_2_deg 5.342 r_mcangle_other 3.974 r_scbond_it 3.974
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.31 r_dihedral_angle_3_deg 12.989 r_lrange_it 7.531 r_lrange_other 7.531 r_dihedral_angle_1_deg 6.135 r_scangle_it 5.981 r_scangle_other 5.98 r_dihedral_angle_2_deg 5.342 r_mcangle_other 3.974 r_scbond_it 3.974 r_mcangle_it 3.973 r_scbond_other 3.945 r_mcbond_it 2.805 r_mcbond_other 2.801 r_angle_refined_deg 1.88 r_angle_other_deg 0.642 r_nbd_refined 0.225 r_symmetry_xyhbond_nbd_refined 0.206 r_nbd_other 0.191 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.188 r_xyhbond_nbd_refined 0.184 r_symmetry_nbd_refined 0.179 r_metal_ion_refined 0.139 r_chiral_restr 0.096 r_symmetry_nbtor_other 0.078 r_dihedral_angle_other_2_deg 0.065 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6892 Nucleic Acid Atoms Solvent Atoms 787 Heterogen Atoms 152
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing