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Crystal Structure of the Coxiella burnetii 2-methylisocitrate lyase Bound to Inhibitor Isocitric Acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 292 Clear Strategy I D7: 0.3 M sodium acetate trihydrate, 0.1 M sodium cacodylate pH 6.5, 8% w/v PEG 20,000, 8% v/v PEG 500 MME
Crystal Properties Matthews coefficient Solvent content 2.56 52.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.785 α = 90 b = 115.55 β = 92.34 c = 195.241 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 EIGER2 XE 16M 2022-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 2.33 59.24 99.98 0.9945 8.29 7.04 177721
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 2.33 2.37 0.2991
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 2.33 59.24 168617 8841 99.83 0.21657 0.214 0.214 0.26523 0.2653 RANDOM 68.925
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] 2.57 1.57 -1.87 -0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.402 r_long_range_B_refined 21.983 r_mcangle_it 18.71 r_dihedral_angle_4_deg 17.295 r_scbond_it 15.816 r_dihedral_angle_3_deg 14.783 r_mcbond_it 14.276 r_dihedral_angle_1_deg 6.113 r_angle_refined_deg 1.195 r_chiral_restr 0.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.402 r_long_range_B_refined 21.983 r_mcangle_it 18.71 r_dihedral_angle_4_deg 17.295 r_scbond_it 15.816 r_dihedral_angle_3_deg 14.783 r_mcbond_it 14.276 r_dihedral_angle_1_deg 6.113 r_angle_refined_deg 1.195 r_chiral_restr 0.096 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 26526 Nucleic Acid Atoms Solvent Atoms 881 Heterogen Atoms 326
Software Software Software Name Purpose REFMAC refinement xia2 data reduction DIALS data reduction Aimless data scaling PHASER phasing