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Glyoxysomal Citrate Synthase 3 from Arabidopsis thaliana in complex with OAA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4G6B polyalanine
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 100mM OAA, 65mM HEPES pH 7.0, 6.5mM MgCl2, 13% (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.53 51.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.084 α = 90 b = 64.726 β = 92.616 c = 192.512 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 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) 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 1.95 48.1 99.6 0.048 12.84 3.4 141350
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 1.95 1.97 0.435
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 1.95 48.1 141350 7090 99.593 0.188 0.186 0.1945 0.225 0.2337 44.838
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] 0.085 0.008 -0.027 -0.059
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.679 r_dihedral_angle_6_deg 14.993 r_lrange_it 8.804 r_lrange_other 8.803 r_dihedral_angle_2_deg 7.054 r_scangle_it 6.694 r_scangle_other 6.693 r_dihedral_angle_1_deg 6.281 r_mcangle_it 5.599 r_mcangle_other 5.599
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.679 r_dihedral_angle_6_deg 14.993 r_lrange_it 8.804 r_lrange_other 8.803 r_dihedral_angle_2_deg 7.054 r_scangle_it 6.694 r_scangle_other 6.693 r_dihedral_angle_1_deg 6.281 r_mcangle_it 5.599 r_mcangle_other 5.599 r_scbond_it 4.409 r_scbond_other 4.409 r_mcbond_it 3.928 r_mcbond_other 3.928 r_angle_refined_deg 1.673 r_angle_other_deg 0.56 r_symmetry_nbd_refined 0.288 r_nbd_other 0.278 r_nbd_refined 0.221 r_symmetry_nbd_other 0.194 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.146 r_symmetry_xyhbond_nbd_refined 0.098 r_chiral_restr 0.082 r_symmetry_nbtor_other 0.077 r_symmetry_xyhbond_nbd_other 0.035 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13643 Nucleic Acid Atoms Solvent Atoms 426 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing