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Crystal structure of 3-nitropropionate modified isocitrate lyase from Mycobacterium tuberculosis with pyruvate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F8I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 50 mM EPPS, 100 mM MgCl2, 17.5%(w/v) PEG4000 (well solution); 10 mg/mL MtICL in 50 mM Tris pH 8.0, 100 mM NaCl, 5 mM MgSO4, 3 mM 3-nitropropionate, and 1 mM DTT (protein solution); 2 uL total drop volume, 1:1 well solution:protein solution
Crystal Properties Matthews coefficient Solvent content 2.14 42.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.67 α = 90 b = 84.32 β = 116.59 c = 156.18 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 PILATUS3 6M 2017-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 APS 23-ID-D
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 72.183 100 0.1711 0.1852 0.996 7.19 6.9 306332 31.44
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 1.864 100 2.637 2.849 0.265 0.52 7
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1F8I 1.8 72.183 1.33 305824 1996 99.77 0.1631 0.1629 0.1974 0.1856 39.7172
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 17.191 f_angle_d 0.801 f_chiral_restr 0.048 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 26498 Nucleic Acid Atoms Solvent Atoms 2721 Heterogen Atoms 299
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction