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Glyoxysomal Citrate Synthase 3 from Arabidopsis thaliana in complex with OAA and MNB
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 293 100mM OAA and 10% volume of a saturated solution of DNTB in 70mM HEPES pH7.0, 7mM MgCl2, 14%(w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.39 48.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 192.336 α = 90 b = 63.55 β = 90 c = 76.595 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 2022-02-08 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) 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 2.29 43.59 98.96 0.2031 8.96 6.3 42621
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 2.29 2.32 1.375
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 2.294 38.915 42383 1988 98.593 0.207 0.2042 0.2061 0.2658 0.2617 47.723
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] -2.662 2.754 -0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.399 r_dihedral_angle_6_deg 14.953 r_lrange_other 11.019 r_lrange_it 11.018 r_dihedral_angle_2_deg 10.968 r_scangle_it 7.889 r_scangle_other 7.888 r_dihedral_angle_1_deg 7.177 r_mcangle_it 7.04 r_mcangle_other 7.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.399 r_dihedral_angle_6_deg 14.953 r_lrange_other 11.019 r_lrange_it 11.018 r_dihedral_angle_2_deg 10.968 r_scangle_it 7.889 r_scangle_other 7.888 r_dihedral_angle_1_deg 7.177 r_mcangle_it 7.04 r_mcangle_other 7.04 r_scbond_it 5.032 r_scbond_other 5.032 r_mcbond_it 4.603 r_mcbond_other 4.603 r_angle_refined_deg 1.714 r_dihedral_angle_other_3_deg 1.132 r_angle_other_deg 0.559 r_nbd_refined 0.231 r_nbd_other 0.212 r_symmetry_nbd_refined 0.208 r_symmetry_nbd_other 0.202 r_symmetry_xyhbond_nbd_other 0.2 r_xyhbond_nbd_refined 0.191 r_nbtor_refined 0.19 r_symmetry_xyhbond_nbd_refined 0.189 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.077 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6574 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing