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Crystal structure of isocitrate lyase and phosphorylmutase:isocitrate lyase from Brucella melitensis biovar Abortus 2308 bound to itaconic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EOL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 287 BrabA.00014.a.A1.PW38950 at 25.5 mg/mL with 2.5 mM itaconic acid and 2.5 mM MgCl2 against MCSG1 screen condition G8: 0.2 M ammonium sulfate, 0.1 M Tris pH 8.5, 25% PEG 3350 supplemented with 20% ethylene glycol as cryo-protectant; crystal tracking ID 321126g8, unique puck ID qrt6-6
Crystal Properties Matthews coefficient Solvent content 2.42 49.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.75 α = 90 b = 136.27 β = 90 c = 181.98 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX-300 2021-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 1.8 47.59 99.4 0.072 0.078 0.998 14.83 6.833 175674 25.21
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 1.8 1.85 99.6 0.539 0.581 0.923 3.36 7.05
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3eol 1.8 47.59 1.35 175615 1913 99.35 0.143 0.1427 0.1428 0.1663 0.1668 31.1116
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.394 f_angle_d 0.781 f_chiral_restr 0.05 f_plane_restr 0.008 f_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12970 Nucleic Acid Atoms Solvent Atoms 1592 Heterogen Atoms 74
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling MOLREP phasing PDB_EXTRACT data extraction