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citrate synthases complexed with oxaloacetate and acetyl-CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5UZR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289.15 0.2 M ammonium acetate pH=7.1, 20% w/v PEG3350
Crystal Properties Matthews coefficient Solvent content 2.1 41.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.523 α = 102.52 b = 59.789 β = 98.23 c = 72.582 γ = 118.76
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 2023-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.979 SSRF BL10U2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.03 67.83 94.2 0.114 0.151 0.978 1.6 2 48136
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.03 2.14 0.841 1.134 0.223
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.1 41.12 41416 2024 93.89 0.23601 0.23298 0.2361 0.29869 0.3036 RANDOM 48.895
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.539 r_long_range_B_refined 7.641 r_long_range_B_other 7.637 r_dihedral_angle_2_deg 6.495 r_dihedral_angle_1_deg 6.201 r_scangle_other 4.249 r_mcangle_it 4.17 r_mcangle_other 4.17 r_mcbond_it 2.564 r_mcbond_other 2.562
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.539 r_long_range_B_refined 7.641 r_long_range_B_other 7.637 r_dihedral_angle_2_deg 6.495 r_dihedral_angle_1_deg 6.201 r_scangle_other 4.249 r_mcangle_it 4.17 r_mcangle_other 4.17 r_mcbond_it 2.564 r_mcbond_other 2.562 r_scbond_it 2.538 r_scbond_other 2.537 r_angle_refined_deg 1.118 r_angle_other_deg 0.398 r_chiral_restr 0.054 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6813 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 121
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing