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Crystal Structure of the Coxiella burnetii 2-methylisocitrate lyase
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 VAPOR DIFFUSION, HANGING DROP 4.2 292 10% v/v EtOH, 0.1 M sodium-citrate pH 4.2, 1% w/w PEG 1000
Crystal Properties Matthews coefficient Solvent content 2.17 43.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.96 α = 90 b = 74.96 β = 90 c = 183.99 γ = 120
Symmetry Space Group P 31 2 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 2024-01-31 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 1.55 64.94 100 0.9998 17.64 20.2 87936
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 1.55 1.58 0.3264
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.6 53.04 73899 3856 97.28 0.23789 0.23484 0.29895 0.2866 RANDOM 57.637
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] 1.18 0.59 1.18 -3.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.657 r_long_range_B_refined 15.823 r_dihedral_angle_4_deg 15.647 r_dihedral_angle_3_deg 14.541 r_mcangle_it 11.949 r_scbond_it 11.034 r_mcbond_it 9.628 r_dihedral_angle_1_deg 6.205 r_angle_refined_deg 1.246 r_chiral_restr 0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.657 r_long_range_B_refined 15.823 r_dihedral_angle_4_deg 15.647 r_dihedral_angle_3_deg 14.541 r_mcangle_it 11.949 r_scbond_it 11.034 r_mcbond_it 9.628 r_dihedral_angle_1_deg 6.205 r_angle_refined_deg 1.246 r_chiral_restr 0.094 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 4503 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement xia2 data reduction DIALS data reduction Aimless data scaling PHASER phasing